Variant report

Variant	rs12450799
Chromosome Location	chr17:17730201-17730202
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:17729606-17731920	K562	blood:	n/a	n/a
2	POLR2A	chr17:17730084-17730202	K562	blood:	n/a	n/a
3	POLR2A	chr17:17729892-17730714	HepG2	liver:	n/a	n/a
4	POLR2A	chr17:17730171-17730328	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr17:17730197-17730204	HepG2	liver:	n/a	n/a
6	POLR2A	chr17:17730144-17730418	HCT-116	colon:	n/a	n/a
7	ZKSCAN1	chr17:17730126-17730446	Hela-S3	cervix:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17729263..17731317-chr17:17786553..17789397,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TOM1L2-2	chr17:17729614-17730489	NONHSAT146115

No data

Variant related genes	Relation type
SREBF1	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1052299	0.81[EUR][1000 genomes]
rs11078399	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1108648	0.81[EUR][1000 genomes]
rs11652144	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11656665	0.89[AMR][1000 genomes]
rs11657130	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11657423	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12936037	0.80[AMR][1000 genomes]
rs12938501	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12941039	0.83[AMR][1000 genomes]
rs12943500	0.82[AMR][1000 genomes]
rs12946746	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12952723	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13306736	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16960744	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1889014	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1889018	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2236513	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3183702	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3744113	0.81[EUR][1000 genomes]
rs3744115	0.81[EUR][1000 genomes]
rs4924821	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4924822	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4925116	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925117	0.87[ASN][1000 genomes]
rs4925119	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4925120	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56248913	0.88[AMR][1000 genomes]
rs7359509	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7503747	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8065497	0.84[AMR][1000 genomes]
rs8066560	0.86[EUR][1000 genomes]
rs8078756	0.82[EUR][1000 genomes]
rs9891957	0.82[EUR][1000 genomes]
rs9895750	0.80[AMR][1000 genomes]
rs9899634	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9902941	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9906673	0.81[EUR][1000 genomes]
rs9915248	0.81[EUR][1000 genomes]
rs9915776	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:34 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
4	nsv907752	chr17:17569012-17750907	Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
5	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
6	nsv907753	chr17:17573539-17747289	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
7	nsv907754	chr17:17573539-17782404	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
8	nsv1061126	chr17:17578826-17803194	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
9	nsv543238	chr17:17578826-17803194	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	nsv833385	chr17:17594037-17765578	Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
11	nsv1058884	chr17:17594370-17803194	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
12	nsv543240	chr17:17594370-17803194	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
13	nsv1064176	chr17:17596222-17803194	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
14	nsv543242	chr17:17596222-17803194	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
15	nsv1062361	chr17:17598407-17746899	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
16	nsv543243	chr17:17598407-17746899	Genic enhancers Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
17	nsv907756	chr17:17619859-17747289	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
18	nsv522668	chr17:17619859-17752809	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
19	nsv907757	chr17:17619859-17752809	Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
20	nsv907758	chr17:17619859-17782404	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
21	nsv907759	chr17:17619859-17802478	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
22	nsv1059949	chr17:17632590-17803194	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
23	nsv543244	chr17:17632590-17803194	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
24	nsv907760	chr17:17649423-17782404	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
25	nsv907761	chr17:17649423-17802478	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
26	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
27	nsv907762	chr17:17668071-17802478	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
28	nsv907763	chr17:17673824-17749822	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
29	nsv907764	chr17:17673824-17754633	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
30	nsv907765	chr17:17682484-17802478	Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
31	nsv907766	chr17:17682484-17957348	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
32	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
33	nsv907767	chr17:17709136-17733760	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
34	nsv907768	chr17:17709136-17747289	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12450799	SREBF1	cis	Whole Blood	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17727000-17732200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr17:17727200-17730400	Enhancers	Spleen	Spleen
3	chr17:17727600-17730400	Enhancers	Primary B cells from cord blood	blood
4	chr17:17727600-17730400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr17:17727600-17730400	Enhancers	Left Ventricle	heart
6	chr17:17727600-17730400	Enhancers	Pancreas	Pancrea
7	chr17:17727600-17730400	Enhancers	HUVEC	blood vessel
8	chr17:17727600-17730600	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr17:17727600-17730600	Enhancers	Psoas Muscle	Psoas
10	chr17:17727600-17730800	Enhancers	Esophagus	oesophagus
11	chr17:17727600-17731000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr17:17727600-17731400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr17:17727600-17731800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr17:17727600-17734400	Enhancers	Placenta	Placenta
15	chr17:17727600-17736400	Enhancers	Liver	Liver
16	chr17:17727800-17730400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr17:17727800-17730400	Genic enhancers	Fetal Intestine Small	intestine
18	chr17:17727800-17730400	Enhancers	Fetal Muscle Trunk	muscle
19	chr17:17727800-17730400	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr17:17727800-17730400	Enhancers	GM12878-XiMat	blood
21	chr17:17727800-17730800	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr17:17727800-17731000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr17:17727800-17731400	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr17:17727800-17731400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr17:17727800-17731800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr17:17727800-17732200	Enhancers	Primary T cells fromperipheralblood	blood
27	chr17:17727800-17732400	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr17:17728000-17730600	Enhancers	Duodenum Mucosa	Duodenum
29	chr17:17728000-17730800	Enhancers	Brain Hippocampus Middle	brain
30	chr17:17728000-17731400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr17:17728000-17732000	Enhancers	Colonic Mucosa	Colon
32	chr17:17728200-17730600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr17:17728200-17730600	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr17:17728200-17731800	Enhancers	Primary hematopoietic stem cells	blood
35	chr17:17728400-17731600	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr17:17728400-17732600	Weak transcription	Fetal Brain Male	brain
37	chr17:17728600-17730600	Enhancers	Colon Smooth Muscle	Colon
38	chr17:17728600-17732800	Weak transcription	Fetal Brain Female	brain
39	chr17:17728600-17734200	Weak transcription	Brain Angular Gyrus	brain
40	chr17:17728600-17734200	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr17:17728600-17734600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr17:17728600-17734800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr17:17728600-17737800	Weak transcription	NH-A	brain
44	chr17:17728600-17738400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr17:17728600-17738400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr17:17728600-17738600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr17:17728600-17738600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr17:17728600-17738800	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr17:17728600-17738800	Weak transcription	Fetal Kidney	kidney
50	chr17:17728800-17733000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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