Variant report

Variant	rs854809
Chromosome Location	chr17:18006539-18006540
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:18005951-18006640	GM12892	blood:	n/a	n/a
2	POLR2A	chr17:18006032-18006585	GM12878	blood:	n/a	n/a
3	POLR2A	chr17:18005959-18008751	K562	blood:	n/a	n/a
4	POLR2A	chr17:18006105-18007901	A549	lung:	n/a	n/a
5	POLR2A	chr17:18006399-18006628	K562	blood:	n/a	n/a
6	POLR2A	chr17:18005949-18006596	GM12878	blood:	n/a	n/a
7	POLR2A	chr17:18006013-18009825	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr17:18005830-18008721	GM12892	blood:	n/a	n/a
9	POLR2A	chr17:18005977-18006580	GM12892	blood:	n/a	n/a
10	POLR2A	chr17:18006212-18006649	GM12891	blood:	n/a	n/a
11	POLR2A	chr17:18006099-18006590	GM12891	blood:	n/a	n/a
12	POLR2A	chr17:18006071-18006580	HL-60	blood:	n/a	n/a
13	POLR2A	chr17:18006495-18006609	K562	blood:	n/a	n/a
14	POLR2A	chr17:18006123-18006548	GM12878	blood:	n/a	n/a
15	POLR2A	chr17:18006381-18007107	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr17:18006478-18006855	Hela-S3	cervix:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:17997353..17998976-chr17:18004637..18006664,2	K562	blood:
2	chr17:18004673..18008844-chr17:18009305..18012045,5	K562	blood:
3	chr17:17995313..17997784-chr17:18005282..18007698,2	K562	blood:
4	chr17:17990264..17992875-chr17:18002923..18006800,4	MCF-7	breast:

No data

Variant related genes	Relation type
DRG2	TF binding region
ENSG00000091536	Chromatin interaction
ENSG00000108591	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1008135	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1101727	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11078408	0.85[CEU][hapmap]
rs11078410	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11650021	0.81[EUR][1000 genomes]
rs11867241	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11870660	0.85[CEU][hapmap]
rs12939020	0.81[EUR][1000 genomes]
rs2056842	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2955350	0.83[EUR][1000 genomes]
rs2955353	0.83[EUR][1000 genomes]
rs2955354	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs2955355	0.95[CEU][hapmap];0.88[GIH][hapmap];0.83[EUR][1000 genomes]
rs2955356	0.95[CEU][hapmap];0.88[GIH][hapmap];0.83[EUR][1000 genomes]
rs2955357	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs2955358	0.95[CEU][hapmap];0.88[GIH][hapmap];0.83[EUR][1000 genomes]
rs2955359	0.95[CEU][hapmap];0.88[GIH][hapmap];0.83[EUR][1000 genomes]
rs2955365	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2955366	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2955367	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2955368	0.84[EUR][1000 genomes]
rs2955370	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs2955372	0.95[CEU][hapmap];0.88[GIH][hapmap];0.84[EUR][1000 genomes]
rs2955377	0.90[CEU][hapmap];0.88[GIH][hapmap]
rs2955378	0.95[CEU][hapmap];0.88[GIH][hapmap]
rs2955380	0.95[CEU][hapmap];0.88[GIH][hapmap];0.83[EUR][1000 genomes]
rs2955381	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs2955383	0.95[CEU][hapmap];0.88[GIH][hapmap];0.81[EUR][1000 genomes]
rs2955384	0.95[CEU][hapmap];0.88[GIH][hapmap];0.82[EUR][1000 genomes]
rs2955385	0.95[CEU][hapmap];0.88[GIH][hapmap];0.82[EUR][1000 genomes]
rs2974998	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2974999	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2975003	0.81[ASN][1000 genomes]
rs2975004	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs2975005	0.81[ASN][1000 genomes]
rs4072738	0.89[CEU][hapmap]
rs4072739	0.89[CEU][hapmap]
rs4299203	0.85[CEU][hapmap]
rs4365346	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4368210	0.95[CEU][hapmap];0.88[GIH][hapmap]
rs4410135	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4426402	1.00[CEU][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4459604	0.95[CEU][hapmap];0.88[GIH][hapmap]
rs4506967	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4506969	0.90[CEU][hapmap]
rs4561528	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4584886	0.95[CEU][hapmap];0.88[GIH][hapmap]
rs4643387	0.84[EUR][1000 genomes]
rs4924832	0.95[CEU][hapmap];0.88[GIH][hapmap]
rs4925135	0.83[EUR][1000 genomes]
rs4925136	0.82[EUR][1000 genomes]
rs59518074	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62073573	0.94[EUR][1000 genomes]
rs6502632	0.95[CEU][hapmap];0.88[GIH][hapmap]
rs6502633	0.82[EUR][1000 genomes]
rs6502636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502637	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6826	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712267	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs712268	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7207461	0.83[EUR][1000 genomes]
rs7207821	0.95[CEU][hapmap]
rs7209003	0.95[CEU][hapmap]
rs7210400	0.83[EUR][1000 genomes]
rs7211714	1.00[CEU][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7212167	0.95[CEU][hapmap];0.88[GIH][hapmap]
rs7212447	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs721669	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219324	0.89[CEU][hapmap]
rs7224047	0.80[EUR][1000 genomes]
rs7406744	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7406982	0.95[CEU][hapmap];0.88[GIH][hapmap];0.80[EUR][1000 genomes]
rs741782	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7503738	0.80[EUR][1000 genomes]
rs8066764	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8068175	0.85[CEU][hapmap]
rs8075189	0.95[CEU][hapmap]
rs8080602	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs854763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854767	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs854768	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs854769	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs854770	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs854789	0.98[EUR][1000 genomes]
rs854790	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs854791	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs854792	0.83[EUR][1000 genomes]
rs854808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854814	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854817	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs854818	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9303144	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9894138	0.83[EUR][1000 genomes]
rs9896837	0.95[CEU][hapmap];0.88[GIH][hapmap]
rs9897761	0.95[CEU][hapmap]
rs9899355	0.89[CEU][hapmap]
rs9913277	0.95[CEU][hapmap];0.88[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv960429	chr17:17951047-18027679	Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription 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 target site	38 gene(s)	inside rSNPs	diseases
6	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
8	nsv907769	chr17:18000321-18064195	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv457697	chr17:18003845-18046290	Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv574527	chr17:18003845-18046290	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv907770	chr17:18003845-18098018	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs854809	SREBF1	cis	Whole Blood	GTEx
rs854809	TOM1L2	cis	parietal	SCAN
rs854809	C17orf39	cis	cerebellum	SCAN
rs854809	TOM1L2	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17991800-18009800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:17992200-18014000	Weak transcription	Right Atrium	heart
3	chr17:17993000-18012000	Strong transcription	Fetal Muscle Trunk	muscle
4	chr17:17993200-18011200	Strong transcription	Fetal Stomach	stomach
5	chr17:17994000-18010800	Strong transcription	Dnd41	blood
6	chr17:17994200-18010800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr17:17994200-18010800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr17:17994200-18011000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:17994200-18011000	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr17:17994200-18011600	Strong transcription	Fetal Muscle Leg	muscle
11	chr17:17994200-18011800	Strong transcription	Stomach Smooth Muscle	stomach
12	chr17:17994200-18012000	Strong transcription	Fetal Intestine Small	intestine
13	chr17:17994400-18011000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr17:17994400-18011400	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr17:17994600-18011200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr17:17994600-18012800	Strong transcription	Thymus	Thymus
17	chr17:17995000-18010800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr17:17995000-18011200	Strong transcription	Placenta	Placenta
19	chr17:17995200-18011000	Strong transcription	Ovary	ovary
20	chr17:17995200-18011000	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr17:17995200-18011000	Strong transcription	NHLF	lung
22	chr17:17995200-18011400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr17:17995200-18011400	Strong transcription	Lung	lung
24	chr17:17995200-18011400	Strong transcription	A549	lung
25	chr17:17995200-18011600	Strong transcription	Fetal Intestine Large	intestine
26	chr17:17995400-18011000	Strong transcription	Adipose Nuclei	Adipose
27	chr17:17995400-18011400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr17:17996000-18010400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr17:17996200-18011000	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr17:17996400-18011000	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr17:17996800-18011000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr17:17996800-18011200	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr17:17997000-18008000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr17:17997000-18010800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr17:17997000-18010800	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr17:17997000-18010800	Strong transcription	Aorta	Aorta
37	chr17:17997000-18010800	Strong transcription	Brain Anterior Caudate	brain
38	chr17:17997000-18011000	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr17:17997000-18011200	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr17:17997200-18011000	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr17:17997600-18007800	Strong transcription	Left Ventricle	heart
42	chr17:17997600-18011000	Weak transcription	Fetal Heart	heart
43	chr17:17997600-18011000	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr17:17997800-18007000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr17:17997800-18007200	Weak transcription	Fetal Kidney	kidney
46	chr17:17997800-18007400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr17:17997800-18008600	Strong transcription	NHEK	skin
48	chr17:17998000-18011000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr17:17998000-18011200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr17:17998000-18011600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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