Variant report

Variant	rs3751979
Chromosome Location	chr17:20160925-20160926
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:20159792..20163252-chr17:20165134..20168652,3	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11868429	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12051550	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs12051844	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12051865	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16942325	0.91[CHB][hapmap]
rs16959946	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs16960700	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16960715	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16960717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16960730	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16960735	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16964352	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.92[ASN][1000 genomes]
rs1971043	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1971044	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2526477	0.83[YRI][hapmap]
rs2703781	0.83[YRI][hapmap]
rs2703805	0.83[YRI][hapmap]
rs28550747	0.90[ASN][1000 genomes]
rs3764436	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs5025290	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.86[ASN][1000 genomes]
rs57110692	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61141789	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61660810	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6587060	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6587061	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587218	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6587221	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7207458	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7211948	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7213349	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7213816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7215097	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7215432	0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7218859	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73299658	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73301548	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73309111	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73981849	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8076627	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8077051	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8077852	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9895295	0.91[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs9896190	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9899514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9901102	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9902683	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs9905976	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9908418	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs9911605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9913018	1.00[CHB][hapmap]
rs9913394	0.91[EUR][1000 genomes]
rs9914219	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9941362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9941376	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1067100	chr17:20007480-20464520	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv543260	chr17:20007480-20464520	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv482830	chr17:20012748-20169153	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv428669	chr17:20071969-20245033	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1064854	chr17:20086562-20225751	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv2761953	chr17:20086562-20225763	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1063833	chr17:20088333-20206601	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv574581	chr17:20088492-20699545	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
13	nsv1065363	chr17:20118499-20162888	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv1059774	chr17:20118499-20163560	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv1062124	chr17:20139384-20206601	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv543261	chr17:20139384-20206601	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	nsv1065758	chr17:20141912-20464366	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
18	nsv543262	chr17:20141912-20464366	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
19	nsv1057389	chr17:20158343-20256498	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3751979	ALDH3A1	cis	parietal	SCAN
rs3751979	AKAP10	cis	Whole Blood	GTEx
rs3751979	CYTSB	cis	parietal	SCAN
rs3751979	SLC47A1	cis	lymphoblastoid	seeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20111600-20166000	Weak transcription	Right Ventricle	heart
2	chr17:20129200-20161600	Weak transcription	Fetal Brain Female	brain
3	chr17:20129600-20161600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:20130600-20161200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr17:20130600-20170000	Weak transcription	K562	blood
6	chr17:20130600-20170200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr17:20131800-20164400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr17:20136200-20161600	Weak transcription	Lung	lung
9	chr17:20136400-20161200	Weak transcription	Fetal Lung	lung
10	chr17:20136400-20209800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr17:20138400-20165200	Weak transcription	Primary B cells from cord blood	blood
12	chr17:20148200-20165000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr17:20148200-20165600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr17:20148400-20161200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr17:20148400-20161600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr17:20148400-20161600	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr17:20148600-20161400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr17:20150400-20161400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr17:20150400-20170200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr17:20150800-20165600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr17:20151200-20164000	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr17:20151600-20161000	Weak transcription	Left Ventricle	heart
23	chr17:20151600-20164400	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr17:20151600-20170800	Weak transcription	GM12878-XiMat	blood
25	chr17:20151600-20190000	Weak transcription	Colonic Mucosa	Colon
26	chr17:20151800-20161000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr17:20151800-20161200	Weak transcription	Pancreas	Pancrea
28	chr17:20151800-20165800	Weak transcription	HMEC	breast
29	chr17:20151800-20167000	Weak transcription	NH-A	brain
30	chr17:20152000-20161000	Weak transcription	Adipose Nuclei	Adipose
31	chr17:20152000-20161200	Weak transcription	NHEK	skin
32	chr17:20152800-20169800	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr17:20152800-20176200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr17:20153000-20161000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr17:20153600-20161600	Weak transcription	Fetal Brain Male	brain
36	chr17:20153600-20161800	Weak transcription	HSMM	muscle
37	chr17:20154400-20161000	Weak transcription	Fetal Intestine Large	intestine
38	chr17:20155000-20162000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr17:20155600-20165200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr17:20155800-20165000	Weak transcription	HUVEC	blood vessel
41	chr17:20156600-20161000	Enhancers	Primary T cells from cord blood	blood
42	chr17:20157000-20161000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr17:20157400-20162400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr17:20157600-20165800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr17:20157800-20161200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr17:20157800-20161200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr17:20157800-20163600	Weak transcription	Esophagus	oesophagus
48	chr17:20158000-20161000	Weak transcription	Gastric	stomach
49	chr17:20158000-20166200	Weak transcription	Fetal Muscle Trunk	muscle
50	chr17:20158200-20165400	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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