Variant report

Variant	rs17273020
Chromosome Location	chr3:17415705-17415706
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	chr3:17415575..17418642-chr3:17419331..17422264,3	MCF-7	breast:

Extended variants
information (count: 164 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:149)

rs_ID	r²[population]
rs10212255	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11713917	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11717644	1.00[ASN][1000 genomes]
rs11720653	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494513	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13093375	1.00[ASN][1000 genomes]
rs13095571	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13317478	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13318609	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13318886	0.88[MEX][hapmap]
rs13320647	0.82[MEX][hapmap]
rs13320693	1.00[ASN][1000 genomes]
rs13321297	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13327810	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs13353435	1.00[ASN][1000 genomes]
rs1374197	0.94[MEX][hapmap]
rs1375817	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs1375818	1.00[JPT][hapmap];0.94[MEX][hapmap]
rs1449881	1.00[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs1449883	1.00[JPT][hapmap]
rs1449884	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1449886	1.00[JPT][hapmap]
rs1463218	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1463221	1.00[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[ASN][1000 genomes]
rs1545424	1.00[JPT][hapmap]
rs1597393	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17043494	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17043539	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17043541	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17200818	0.94[MEX][hapmap]
rs187303	1.00[MEX][hapmap]
rs2060623	0.93[MEX][hapmap]
rs2060624	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2060625	1.00[MEX][hapmap]
rs2060628	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2060629	1.00[JPT][hapmap]
rs2084572	1.00[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2122368	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2247106	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2348001	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2348003	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2470349	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.93[LWK][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470583	1.00[JPT][hapmap]
rs2592099	0.87[MEX][hapmap]
rs2596636	1.00[JPT][hapmap]
rs2596637	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2596638	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs2596639	1.00[JPT][hapmap]
rs2596640	1.00[JPT][hapmap]
rs2596645	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2596646	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2596647	1.00[ASN][1000 genomes]
rs2596656	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2596657	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[ASN][1000 genomes]
rs2596664	1.00[JPT][hapmap]
rs2596665	1.00[JPT][hapmap];0.94[MEX][hapmap]
rs2596666	1.00[ASN][1000 genomes]
rs2596670	1.00[ASN][1000 genomes]
rs2596672	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2596674	1.00[CHB][hapmap]
rs2596678	1.00[MEX][hapmap]
rs2596679	1.00[MEX][hapmap]
rs2596681	1.00[MEX][hapmap]
rs2733479	1.00[MEX][hapmap]
rs2733481	1.00[ASN][1000 genomes]
rs2733485	1.00[JPT][hapmap]
rs2733493	1.00[ASN][1000 genomes]
rs2733494	1.00[ASN][1000 genomes]
rs2733495	1.00[JPT][hapmap]
rs2733497	1.00[JPT][hapmap]
rs2733498	1.00[JPT][hapmap]
rs2733499	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2733500	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs2733501	1.00[JPT][hapmap]
rs2733502	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2733508	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2733509	1.00[ASN][1000 genomes]
rs2733515	0.94[MEX][hapmap]
rs2733516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[ASN][1000 genomes]
rs2733517	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2733518	1.00[JPT][hapmap];0.88[MEX][hapmap]
rs2733519	1.00[ASN][1000 genomes]
rs2733520	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[ASN][1000 genomes]
rs2733521	1.00[JPT][hapmap]
rs2733524	1.00[JPT][hapmap]
rs2733526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[ASN][1000 genomes]
rs2733527	1.00[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[ASN][1000 genomes]
rs2733528	1.00[JPT][hapmap]
rs2733529	1.00[JPT][hapmap];0.87[MEX][hapmap]
rs283907	1.00[MEX][hapmap]
rs283908	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs283911	1.00[ASN][1000 genomes]
rs283917	1.00[JPT][hapmap];0.93[MEX][hapmap]
rs283926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283927	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs283929	0.94[MEX][hapmap]
rs283930	1.00[JPT][hapmap]
rs283935	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs283939	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283940	0.94[MEX][hapmap]
rs283941	0.93[MEX][hapmap]
rs283943	1.00[MEX][hapmap]
rs283944	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs283946	1.00[MEX][hapmap]
rs283947	1.00[MEX][hapmap]
rs283948	1.00[MEX][hapmap]
rs283949	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34502358	1.00[ASN][1000 genomes]
rs34892692	1.00[ASN][1000 genomes]
rs6442681	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6442682	0.94[MEX][hapmap]
rs6442683	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6763593	0.94[MEX][hapmap]
rs6763681	1.00[CHB][hapmap]
rs6772394	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs67851870	1.00[ASN][1000 genomes]
rs6787756	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6788763	1.00[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs6799259	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs728022	1.00[MEX][hapmap]
rs7617933	1.00[JPT][hapmap]
rs7623979	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs7630286	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7630433	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7632989	1.00[ASN][1000 genomes]
rs7644020	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[ASN][1000 genomes]
rs7644389	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs7645756	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7647905	0.94[MEX][hapmap]
rs7648883	1.00[ASN][1000 genomes]
rs7651278	1.00[ASN][1000 genomes]
rs767685	1.00[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs9310523	1.00[ASN][1000 genomes]
rs9810675	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9812199	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[ASN][1000 genomes]
rs9812906	1.00[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs9821318	0.82[MEX][hapmap]
rs9824191	1.00[CHB][hapmap]
rs9847461	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9848610	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs9853571	1.00[ASN][1000 genomes]
rs9854201	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9864494	0.94[MEX][hapmap]
rs9870741	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878954	0.88[MEX][hapmap]
rs9880971	1.00[ASN][1000 genomes]
rs9881089	1.00[ASN][1000 genomes]
rs9881850	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9883518	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876590	chr3:17230884-17604963	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv2755406	chr3:17237396-17589896	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv876591	chr3:17246392-17671992	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv869378	chr3:17338236-17576692	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv915606	chr3:17357042-17668263	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv999568	chr3:17360261-17594750	Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv999460	chr3:17360261-17720103	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv536510	chr3:17360261-17720103	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv428080	chr3:17367870-17539943	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv876592	chr3:17369313-17604963	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	esv2755442	chr3:17372796-17589896	Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription 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	3 gene(s)	inside rSNPs	diseases
12	nsv589842	chr3:17381380-17538921	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv1009700	chr3:17391240-17486671	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv470439	chr3:17394615-17538921	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv589843	chr3:17412690-17525505	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17339400-17442200	Weak transcription	Fetal Intestine Small	intestine
2	chr3:17344400-17439000	Weak transcription	Aorta	Aorta
3	chr3:17398800-17430200	Weak transcription	Pancreas	Pancrea
4	chr3:17398800-17447000	Weak transcription	Fetal Stomach	stomach
5	chr3:17401600-17432600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr3:17402400-17443200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:17402600-17451000	Weak transcription	Gastric	stomach
8	chr3:17403000-17443000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:17403200-17449200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:17403400-17442200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:17404200-17449200	Weak transcription	Esophagus	oesophagus
12	chr3:17405000-17432400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:17406400-17442000	Weak transcription	Lung	lung
14	chr3:17407600-17443400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:17407800-17419400	Weak transcription	Brain Hippocampus Middle	brain
16	chr3:17409200-17430800	Weak transcription	Fetal Muscle Leg	muscle
17	chr3:17409200-17435000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:17410000-17426800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr3:17410200-17445200	Weak transcription	Right Ventricle	heart
20	chr3:17410200-17445600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:17410200-17447200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:17410200-17451400	Weak transcription	Brain Angular Gyrus	brain
23	chr3:17410400-17443400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:17410400-17447800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:17410600-17418400	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr3:17411000-17418400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr3:17411200-17418400	Strong transcription	Primary B cells from peripheral blood	blood
28	chr3:17411200-17467400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:17411600-17424000	Weak transcription	Spleen	Spleen
30	chr3:17411600-17425200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:17411600-17430800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr3:17411600-17442000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr3:17411600-17443400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:17411800-17449200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr3:17412000-17418200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:17412200-17432200	Weak transcription	NH-A	brain
37	chr3:17412200-17437800	Weak transcription	GM12878-XiMat	blood
38	chr3:17412400-17416600	Strong transcription	Primary B cells from cord blood	blood
39	chr3:17412600-17416200	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr3:17412800-17450600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr3:17413000-17422000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:17413000-17443400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr3:17413400-17445000	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr3:17413400-17453400	Weak transcription	Psoas Muscle	Psoas
45	chr3:17413600-17430200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:17413600-17430600	Weak transcription	Primary T cells from cord blood	blood
47	chr3:17413600-17430800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:17413600-17430800	Weak transcription	Left Ventricle	heart
49	chr3:17413600-17431000	Weak transcription	Placenta	Placenta
50	chr3:17413600-17432400	Weak transcription	Ovary	ovary

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