Variant report

Variant	rs979182
Chromosome Location	chr5:74832919-74832920
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	chr5:74819271..74821743-chr5:74831867..74834038,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10036682	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10038945	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10041470	0.85[EUR][1000 genomes]
rs10055011	0.85[CHD][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs10059022	0.80[CHD][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs10061689	0.88[EUR][1000 genomes]
rs10067900	0.85[EUR][1000 genomes]
rs10074747	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10076819	0.88[EUR][1000 genomes]
rs10077427	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10078671	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10474437	0.90[EUR][1000 genomes]
rs12173076	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes]
rs13360099	0.90[EUR][1000 genomes]
rs13361353	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1469051	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1553234	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1820049	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1909719	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2287710	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs253387	1.00[JPT][hapmap]
rs253388	0.84[CHD][hapmap]
rs253410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs28408106	0.85[EUR][1000 genomes]
rs28612248	0.89[EUR][1000 genomes]
rs28668361	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28874007	0.90[EUR][1000 genomes]
rs34339	0.94[ASN][1000 genomes]
rs34342	0.94[ASN][1000 genomes]
rs34343	0.94[ASN][1000 genomes]
rs34349	0.89[ASN][1000 genomes]
rs34355	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs34356	1.00[JPT][hapmap]
rs34357	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs3804231	0.95[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs4703671	0.83[EUR][1000 genomes]
rs4703675	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4704213	0.85[EUR][1000 genomes]
rs4704229	0.88[CHD][hapmap];0.92[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56859362	0.90[EUR][1000 genomes]
rs5744544	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5744545	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5744636	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5744667	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5744704	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5744709	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5744712	0.87[CHD][hapmap];0.85[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57907925	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58519566	0.85[EUR][1000 genomes]
rs58841453	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61303403	0.81[EUR][1000 genomes]
rs6891560	0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs72633964	0.85[EUR][1000 genomes]
rs72633965	0.85[EUR][1000 genomes]
rs72633967	0.83[EUR][1000 genomes]
rs72633968	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72633969	0.88[EUR][1000 genomes]
rs72633970	0.90[EUR][1000 genomes]
rs72633971	0.89[EUR][1000 genomes]
rs72633972	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72633973	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72633974	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72633975	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72633976	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72633977	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7356633	0.85[EUR][1000 genomes]
rs7726478	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs904743	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9293652	0.85[EUR][1000 genomes]
rs9293654	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9293655	0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882193	chr5:74656175-74917862	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv882195	chr5:74678937-74896798	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv882196	chr5:74678937-74917862	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv882197	chr5:74692776-74946455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv882198	chr5:74736065-74896798	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv882199	chr5:74757758-74946455	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv882201	chr5:74787310-74890618	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
10	nsv882202	chr5:74808417-74946455	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	esv3385195	chr5:74810245-74843686	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv882203	chr5:74811497-74832919	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv882204	chr5:74811497-74856142	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv882205	chr5:74811497-74862921	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs979182	GCNT4	cis	cerebellum	SCAN
rs979182	ARSB	cis	parietal	SCAN
rs979182	TNPO1	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74808800-74849600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr5:74809600-74839400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr5:74810400-74862400	Weak transcription	Hela-S3	cervix
4	chr5:74818200-74897400	Weak transcription	Thymus	Thymus
5	chr5:74819400-74846800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr5:74822800-74896000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr5:74826000-74862400	Weak transcription	Fetal Heart	heart
8	chr5:74829200-74833000	Enhancers	NHEK	skin
9	chr5:74830000-74833000	Enhancers	HMEC	breast
10	chr5:74830800-74833000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:74831000-74848000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr5:74831000-74852600	Weak transcription	Aorta	Aorta
13	chr5:74831000-74859000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr5:74831000-74862400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr5:74831200-74835200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:74831200-74848200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr5:74831200-74848600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr5:74831200-74877200	Weak transcription	Fetal Kidney	kidney
19	chr5:74831400-74839400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:74831400-74839800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr5:74831400-74845600	Weak transcription	Fetal Lung	lung
22	chr5:74831400-74847400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr5:74831400-74848000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:74831400-74848000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:74831400-74848000	Weak transcription	Liver	Liver
26	chr5:74831400-74848200	Weak transcription	Fetal Intestine Large	intestine
27	chr5:74831400-74848400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr5:74831400-74848600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr5:74831400-74848600	Weak transcription	HSMMtube	muscle
30	chr5:74831600-74836200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:74831600-74839600	Weak transcription	Fetal Muscle Leg	muscle
32	chr5:74831800-74833000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:74831800-74833000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:74831800-74833000	Enhancers	Dnd41	blood
35	chr5:74831800-74833000	Enhancers	K562	blood
36	chr5:74831800-74833200	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr5:74831800-74833400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:74831800-74839400	Weak transcription	Primary T cells from cord blood	blood
39	chr5:74831800-74849200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr5:74832000-74833000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:74832000-74833000	ZNF genes & repeats	Fetal Stomach	stomach
42	chr5:74832000-74833000	Genic enhancers	Pancreas	Pancrea
43	chr5:74832000-74833000	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr5:74832000-74833000	Enhancers	A549	lung
45	chr5:74832000-74833200	Weak transcription	Fetal Brain Female	brain
46	chr5:74832000-74833200	Genic enhancers	Lung	lung
47	chr5:74832000-74833400	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr5:74832000-74833400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:74832000-74833400	Strong transcription	Fetal Intestine Small	intestine
50	chr5:74832000-74833400	Enhancers	Left Ventricle	heart

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