Variant report

Variant	rs1108646
Chromosome Location	chr17:17751478-17751479
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17748813..17751782-chr17:17752295..17755701,3	MCF-7	breast:
2	chr17:17748850..17751713-chr17:17788602..17790581,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175662	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1052299	0.81[EUR][1000 genomes]
rs11078400	0.84[ASN][1000 genomes]
rs1108648	0.81[EUR][1000 genomes]
rs11658309	0.85[ASN][1000 genomes]
rs16960744	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2236513	0.83[EUR][1000 genomes]
rs3183702	0.83[EUR][1000 genomes]
rs35451946	0.86[ASN][1000 genomes]
rs3744113	0.81[EUR][1000 genomes]
rs3744115	0.81[EUR][1000 genomes]
rs4924822	0.83[EUR][1000 genomes]
rs4924823	0.86[ASN][1000 genomes]
rs4925119	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4925120	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4925125	0.88[ASN][1000 genomes]
rs8078756	0.81[EUR][1000 genomes]
rs8079321	0.86[ASN][1000 genomes]
rs8080061	0.88[ASN][1000 genomes]
rs9891957	0.80[EUR][1000 genomes]
rs9893690	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9906673	0.80[EUR][1000 genomes]
rs9907287	0.88[ASN][1000 genomes]
rs9908017	0.88[ASN][1000 genomes]
rs9911281	0.86[ASN][1000 genomes]
rs9915248	0.81[EUR][1000 genomes]
rs9915776	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1108646	SREBF1	cis	Whole Blood	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17743000-17753000	Weak transcription	Fetal Kidney	kidney
2	chr17:17744400-17751800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr17:17744400-17752400	Weak transcription	Primary B cells from cord blood	blood
4	chr17:17744400-17756200	Weak transcription	Aorta	Aorta
5	chr17:17744400-17771400	Weak transcription	Fetal Brain Male	brain
6	chr17:17744600-17752400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr17:17744600-17752600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr17:17744800-17751800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr17:17744800-17753000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr17:17744800-17753000	Weak transcription	NH-A	brain
11	chr17:17745000-17752000	Weak transcription	HSMM	muscle
12	chr17:17745000-17752600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr17:17745200-17751600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr17:17745200-17751800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr17:17745200-17753200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr17:17745200-17753800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr17:17745200-17770600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr17:17745400-17752400	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr17:17745400-17753200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr17:17746000-17752000	Weak transcription	Stomach Mucosa	stomach
21	chr17:17746200-17751800	Weak transcription	Left Ventricle	heart
22	chr17:17746200-17752000	Weak transcription	Pancreas	Pancrea
23	chr17:17746200-17752600	Weak transcription	Hela-S3	cervix
24	chr17:17746800-17752000	Weak transcription	Fetal Lung	lung
25	chr17:17747400-17752800	Strong transcription	Fetal Stomach	stomach
26	chr17:17747800-17752000	Weak transcription	Fetal Heart	heart
27	chr17:17748000-17751600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr17:17748000-17751600	Weak transcription	HepG2	liver
29	chr17:17748200-17755800	Enhancers	Fetal Thymus	thymus
30	chr17:17748400-17751800	Genic enhancers	Lung	lung
31	chr17:17748400-17752200	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr17:17748800-17751800	Weak transcription	Brain Substantia Nigra	brain
33	chr17:17748800-17752000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr17:17748800-17755400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr17:17749000-17751600	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr17:17749000-17752000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr17:17749000-17752000	Strong transcription	Esophagus	oesophagus
38	chr17:17749200-17751800	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr17:17749200-17752200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr17:17749200-17755400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr17:17749200-17755400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr17:17749400-17751800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr17:17749400-17752000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr17:17749400-17752000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr17:17749400-17752000	Strong transcription	NHLF	lung
46	chr17:17749400-17760200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr17:17749600-17751800	Strong transcription	Fetal Muscle Leg	muscle
48	chr17:17749600-17752000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr17:17749800-17752600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr17:17749800-17753000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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