Variant report

Variant	rs2060626
Chromosome Location	chr3:17339260-17339261
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:17330285..17331951-chr3:17337409..17339614,2	MCF-7	breast:
2	chr3:17337522..17339707-chr3:17345126..17347207,2	K562	blood:

Extended variants
information (count: 170 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:165)

rs_ID	r²[population]
rs11713917	0.84[EUR][1000 genomes]
rs12488093	0.84[EUR][1000 genomes]
rs12493567	0.81[EUR][1000 genomes]
rs12494513	0.81[EUR][1000 genomes]
rs13093375	0.82[EUR][1000 genomes]
rs13318609	0.84[EUR][1000 genomes]
rs13322641	0.84[EUR][1000 genomes]
rs13353435	0.82[EUR][1000 genomes]
rs1375817	0.87[EUR][1000 genomes]
rs1375818	0.86[EUR][1000 genomes]
rs1449879	0.87[EUR][1000 genomes]
rs1449881	0.88[EUR][1000 genomes]
rs1449882	0.80[EUR][1000 genomes]
rs1449883	0.84[EUR][1000 genomes]
rs1449884	0.87[EUR][1000 genomes]
rs1449886	0.87[EUR][1000 genomes]
rs1463218	0.88[EUR][1000 genomes]
rs1463221	0.82[EUR][1000 genomes]
rs1470667	0.80[EUR][1000 genomes]
rs1545424	0.87[EUR][1000 genomes]
rs1597393	0.87[EUR][1000 genomes]
rs1597394	0.87[EUR][1000 genomes]
rs17043422	0.84[EUR][1000 genomes]
rs17043492	0.84[EUR][1000 genomes]
rs17043494	0.83[EUR][1000 genomes]
rs17043539	0.81[EUR][1000 genomes]
rs17043541	0.81[EUR][1000 genomes]
rs187303	0.86[EUR][1000 genomes]
rs2060623	0.81[EUR][1000 genomes]
rs2060624	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2060625	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2060627	0.88[EUR][1000 genomes]
rs2060628	0.87[EUR][1000 genomes]
rs2060629	0.87[EUR][1000 genomes]
rs2084572	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2122368	0.87[EUR][1000 genomes]
rs2167118	0.83[EUR][1000 genomes]
rs2167119	0.86[EUR][1000 genomes]
rs2247106	0.87[EUR][1000 genomes]
rs2252237	0.87[EUR][1000 genomes]
rs2348001	0.84[EUR][1000 genomes]
rs2348003	0.88[EUR][1000 genomes]
rs2470347	0.89[EUR][1000 genomes]
rs2470577	0.89[EUR][1000 genomes]
rs2470580	0.84[EUR][1000 genomes]
rs2470581	0.81[EUR][1000 genomes]
rs2470583	0.87[EUR][1000 genomes]
rs2592099	0.84[EUR][1000 genomes]
rs2596636	0.88[EUR][1000 genomes]
rs2596637	0.88[EUR][1000 genomes]
rs2596638	0.88[EUR][1000 genomes]
rs2596639	0.88[EUR][1000 genomes]
rs2596640	0.88[EUR][1000 genomes]
rs2596645	0.88[EUR][1000 genomes]
rs2596646	0.88[EUR][1000 genomes]
rs2596647	0.88[EUR][1000 genomes]
rs2596652	0.84[EUR][1000 genomes]
rs2596657	0.82[EUR][1000 genomes]
rs2596658	0.81[EUR][1000 genomes]
rs2596663	0.80[EUR][1000 genomes]
rs2596664	0.84[EUR][1000 genomes]
rs2596665	0.87[EUR][1000 genomes]
rs2596666	0.87[EUR][1000 genomes]
rs2596667	0.87[EUR][1000 genomes]
rs2596669	0.87[EUR][1000 genomes]
rs2596670	0.86[EUR][1000 genomes]
rs2596671	0.87[EUR][1000 genomes]
rs2596672	0.87[EUR][1000 genomes]
rs2596673	0.86[EUR][1000 genomes]
rs2596674	0.88[EUR][1000 genomes]
rs2596675	0.89[EUR][1000 genomes]
rs2596677	0.88[EUR][1000 genomes]
rs2596678	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2596679	0.89[EUR][1000 genomes]
rs2596680	0.89[EUR][1000 genomes]
rs2596681	0.89[EUR][1000 genomes]
rs2733478	0.89[EUR][1000 genomes]
rs2733479	0.88[EUR][1000 genomes]
rs2733481	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2733485	0.89[EUR][1000 genomes]
rs2733487	0.89[EUR][1000 genomes]
rs2733489	0.80[EUR][1000 genomes]
rs2733491	0.88[EUR][1000 genomes]
rs2733493	0.88[EUR][1000 genomes]
rs2733494	0.88[EUR][1000 genomes]
rs2733497	0.87[EUR][1000 genomes]
rs2733498	0.87[EUR][1000 genomes]
rs2733499	0.87[EUR][1000 genomes]
rs2733500	0.87[EUR][1000 genomes]
rs2733501	0.87[EUR][1000 genomes]
rs2733502	0.87[EUR][1000 genomes]
rs2733504	0.82[EUR][1000 genomes]
rs2733507	0.85[EUR][1000 genomes]
rs2733508	0.84[EUR][1000 genomes]
rs2733509	0.87[EUR][1000 genomes]
rs2733510	0.86[EUR][1000 genomes]
rs2733514	0.89[EUR][1000 genomes]
rs2733515	0.81[EUR][1000 genomes]
rs2733516	0.84[EUR][1000 genomes]
rs2733517	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2733518	0.83[EUR][1000 genomes]
rs2733519	0.84[EUR][1000 genomes]
rs2733520	0.82[EUR][1000 genomes]
rs2733521	0.82[EUR][1000 genomes]
rs2733523	0.89[EUR][1000 genomes]
rs2733524	0.89[EUR][1000 genomes]
rs2733526	0.82[EUR][1000 genomes]
rs2733527	0.81[EUR][1000 genomes]
rs2733528	0.82[EUR][1000 genomes]
rs2733530	0.82[EUR][1000 genomes]
rs283906	0.88[EUR][1000 genomes]
rs283907	0.88[EUR][1000 genomes]
rs283908	0.88[EUR][1000 genomes]
rs283909	0.88[EUR][1000 genomes]
rs283911	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs283912	0.88[EUR][1000 genomes]
rs283913	0.88[EUR][1000 genomes]
rs283914	0.82[EUR][1000 genomes]
rs283915	0.88[EUR][1000 genomes]
rs283916	0.88[EUR][1000 genomes]
rs283917	0.85[EUR][1000 genomes]
rs283918	0.89[EUR][1000 genomes]
rs283919	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs283921	0.88[EUR][1000 genomes]
rs283922	0.89[EUR][1000 genomes]
rs283923	0.89[EUR][1000 genomes]
rs283925	0.89[EUR][1000 genomes]
rs283927	0.86[EUR][1000 genomes]
rs283931	0.85[EUR][1000 genomes]
rs283935	0.84[EUR][1000 genomes]
rs283937	0.83[EUR][1000 genomes]
rs283938	0.86[EUR][1000 genomes]
rs283941	0.86[EUR][1000 genomes]
rs283943	0.86[EUR][1000 genomes]
rs283944	0.86[EUR][1000 genomes]
rs283946	0.86[EUR][1000 genomes]
rs283947	0.86[EUR][1000 genomes]
rs283948	0.86[EUR][1000 genomes]
rs283949	0.86[EUR][1000 genomes]
rs28408438	0.84[EUR][1000 genomes]
rs28454413	0.84[EUR][1000 genomes]
rs34502358	0.84[EUR][1000 genomes]
rs35126965	0.80[EUR][1000 genomes]
rs35234876	0.82[EUR][1000 genomes]
rs4582042	0.83[EUR][1000 genomes]
rs4615062	0.82[EUR][1000 genomes]
rs58307801	0.86[EUR][1000 genomes]
rs62245860	0.84[EUR][1000 genomes]
rs62245914	0.84[EUR][1000 genomes]
rs6442679	0.84[EUR][1000 genomes]
rs6442680	0.82[EUR][1000 genomes]
rs6785870	0.84[EUR][1000 genomes]
rs6799259	0.81[EUR][1000 genomes]
rs723813	0.82[EUR][1000 genomes]
rs728022	0.88[EUR][1000 genomes]
rs7617933	0.83[EUR][1000 genomes]
rs7623979	0.82[EUR][1000 genomes]
rs7630286	0.84[EUR][1000 genomes]
rs7630433	0.84[EUR][1000 genomes]
rs7636787	0.82[EUR][1000 genomes]
rs7642719	0.82[EUR][1000 genomes]
rs7645756	0.84[EUR][1000 genomes]
rs7648883	0.82[EUR][1000 genomes]
rs767685	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9861749	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876589	chr3:17230884-17346355	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	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
3	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
4	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
5	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

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17255200-17363800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:17298800-17373000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:17319800-17351200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:17321600-17354200	Weak transcription	Placenta	Placenta
5	chr3:17322200-17342800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:17327800-17343000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:17328400-17341400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:17328800-17343800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:17329000-17340400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:17329000-17342000	Weak transcription	HSMM	muscle
11	chr3:17329000-17344200	Weak transcription	Psoas Muscle	Psoas
12	chr3:17329200-17343000	Weak transcription	Brain Anterior Caudate	brain
13	chr3:17329200-17344400	Weak transcription	Brain Substantia Nigra	brain
14	chr3:17329600-17342000	Weak transcription	Fetal Thymus	thymus
15	chr3:17330000-17341600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:17330600-17355400	Weak transcription	Left Ventricle	heart
17	chr3:17330800-17341800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:17330800-17350600	Weak transcription	Pancreas	Pancrea
19	chr3:17330800-17350800	Weak transcription	Spleen	Spleen
20	chr3:17330800-17381400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:17331000-17341600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr3:17331000-17344600	Weak transcription	Right Ventricle	heart
23	chr3:17331000-17345000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:17331000-17349200	Weak transcription	Lung	lung
25	chr3:17331000-17350000	Weak transcription	Fetal Stomach	stomach
26	chr3:17331200-17356000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:17331400-17341600	Weak transcription	Primary T cells from cord blood	blood
28	chr3:17331600-17353200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:17333000-17360400	Weak transcription	GM12878-XiMat	blood
30	chr3:17333400-17341600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:17333400-17342000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr3:17333400-17342000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:17333400-17347400	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr3:17333400-17351400	Weak transcription	Fetal Lung	lung
35	chr3:17333400-17357400	Weak transcription	Fetal Intestine Large	intestine
36	chr3:17333400-17357600	Weak transcription	Adipose Nuclei	Adipose
37	chr3:17333400-17363400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:17333400-17372000	Weak transcription	Liver	Liver
39	chr3:17333400-17376000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr3:17333600-17339400	Weak transcription	Primary B cells from peripheral blood	blood
41	chr3:17333600-17341400	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr3:17333600-17341800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:17333600-17351600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:17333600-17354600	Weak transcription	Fetal Muscle Leg	muscle
45	chr3:17333800-17339800	Weak transcription	Primary B cells from cord blood	blood
46	chr3:17333800-17341600	Weak transcription	Dnd41	blood
47	chr3:17334600-17355200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:17337600-17343600	Weak transcription	Aorta	Aorta
49	chr3:17338400-17340600	Strong transcription	Primary hematopoietic stem cells	blood
50	chr3:17338800-17339400	Strong transcription	Fetal Intestine Small	intestine

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