Variant report

Variant	rs2924809
Chromosome Location	chr2:234385709-234385710
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234377261..234380113-chr2:234384331..234386065,2	MCF-7	breast:
2	chr2:234384920..234387471-chr2:234750794..234752642,2	MCF-7	breast:
3	chr2:234372522..234374797-chr2:234385082..234387543,2	MCF-7	breast:
4	chr2:234382281..234385759-chr2:234386993..234388960,3	MCF-7	breast:
5	chr2:234379094..234382048-chr2:234385373..234387118,2	K562	blood:
6	chr2:234385374..234387769-chr2:234390767..234392853,2	K562	blood:
7	chr2:234385429..234386965-chr2:234599786..234601809,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167165	Chromatin interaction

Extended variants
information (count: 129 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10168794	1.00[JPT][hapmap]
rs10169180	0.91[EUR][1000 genomes]
rs10177112	1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs10178062	0.92[EUR][1000 genomes]
rs10178357	0.92[EUR][1000 genomes]
rs10183033	0.92[EUR][1000 genomes]
rs10185923	0.92[EUR][1000 genomes]
rs10193542	1.00[JPT][hapmap]
rs10198879	0.90[EUR][1000 genomes]
rs10207915	0.93[EUR][1000 genomes]
rs10208361	0.92[EUR][1000 genomes]
rs1037451	1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs10803653	0.89[EUR][1000 genomes]
rs10929195	0.92[EUR][1000 genomes]
rs10929200	0.91[EUR][1000 genomes]
rs10929208	1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs1097929	0.93[EUR][1000 genomes]
rs1097930	1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs1097931	1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs11690686	0.93[EUR][1000 genomes]
rs11892545	1.00[JPT][hapmap]
rs1220430	1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs12467878	1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs12473743	0.91[EUR][1000 genomes]
rs12473824	1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs12615446	0.92[EUR][1000 genomes]
rs12692193	0.96[EUR][1000 genomes]
rs12692195	0.92[EUR][1000 genomes]
rs13002253	0.92[EUR][1000 genomes]
rs13018364	0.89[EUR][1000 genomes]
rs13384932	1.00[JPT][hapmap]
rs13391864	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs13393578	0.96[ASN][1000 genomes]
rs13400563	1.00[JPT][hapmap]
rs13403667	1.00[CHB][hapmap]
rs13406462	1.00[CHB][hapmap]
rs13414407	1.00[CHB][hapmap]
rs13425849	1.00[CHB][hapmap]
rs1377459	0.92[EUR][1000 genomes]
rs1377461	0.89[EUR][1000 genomes]
rs1453321	0.91[EUR][1000 genomes]
rs1470864	1.00[CHB][hapmap];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1470865	0.91[EUR][1000 genomes]
rs1542325	1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs1542326	0.91[EUR][1000 genomes]
rs1545525	0.91[EUR][1000 genomes]
rs1597940	1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs1901812	1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs2034675	0.91[EUR][1000 genomes]
rs2124045	1.00[JPT][hapmap];0.98[EUR][1000 genomes]
rs2167884	1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs2167885	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2305541	0.91[ASN][1000 genomes]
rs2602387	0.93[EUR][1000 genomes]
rs2602389	0.93[EUR][1000 genomes]
rs2603545	1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs2603546	0.93[EUR][1000 genomes]
rs2603547	1.00[CHB][hapmap];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28588417	0.96[ASN][1000 genomes]
rs28969983	1.00[CHB][hapmap]
rs2924810	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2924811	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2924813	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2971861	0.96[EUR][1000 genomes]
rs2971862	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2971863	1.00[CHB][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2971864	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2971865	1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2971866	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2971867	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2971869	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2971870	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2971871	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2971872	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2971873	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4047187	0.91[EUR][1000 genomes]
rs4047188	0.94[EUR][1000 genomes]
rs4047198	1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs4047199	1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs4233627	0.93[EUR][1000 genomes]
rs4663684	0.92[EUR][1000 genomes]
rs4663698	1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs55679565	0.92[EUR][1000 genomes]
rs59160392	0.90[EUR][1000 genomes]
rs59458664	0.89[ASN][1000 genomes]
rs6710645	1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs6710772	0.92[EUR][1000 genomes]
rs6716988	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs6720619	1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs6726184	1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs6753062	0.90[EUR][1000 genomes]
rs6756068	1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs73117559	0.94[ASN][1000 genomes]
rs7422734	1.00[JPT][hapmap]
rs7557849	0.93[EUR][1000 genomes]
rs7562752	1.00[CHB][hapmap]
rs7567713	0.92[EUR][1000 genomes]
rs7571288	0.92[EUR][1000 genomes]
rs7572257	1.00[CHB][hapmap]
rs7572310	0.89[EUR][1000 genomes]
rs7575694	0.89[EUR][1000 genomes]
rs7578898	0.92[EUR][1000 genomes]
rs7583222	1.00[CHB][hapmap]
rs7583771	1.00[CHB][hapmap]
rs7587535	1.00[CHB][hapmap]
rs7599285	0.93[EUR][1000 genomes]
rs7603410	0.91[EUR][1000 genomes]
rs7604337	0.83[EUR][1000 genomes]
rs7724	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs838543	1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs838544	0.93[EUR][1000 genomes]
rs838545	0.93[EUR][1000 genomes]
rs838548	0.93[EUR][1000 genomes]
rs838549	0.93[EUR][1000 genomes]
rs838550	1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs838551	0.93[EUR][1000 genomes]
rs838552	1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs838555	0.93[EUR][1000 genomes]
rs838557	1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs838558	1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs838559	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs838561	1.00[JPT][hapmap];0.98[EUR][1000 genomes]
rs838562	1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs860794	0.91[EUR][1000 genomes]
rs896833	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv1000870	chr2:234333083-234410768	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv876013	chr2:234338227-234579915	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv3214	chr2:234384436-234416949	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234339600-234394200	Weak transcription	HUVEC	blood vessel
2	chr2:234339800-234391400	Weak transcription	NHDF-Ad	bronchial
3	chr2:234343000-234393000	Strong transcription	Primary T cells from cord blood	blood
4	chr2:234343000-234402200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:234361200-234389800	Weak transcription	Fetal Kidney	kidney
6	chr2:234363800-234390600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:234364000-234411200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:234365800-234393600	Weak transcription	Hela-S3	cervix
9	chr2:234373000-234392200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:234373000-234409800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:234373400-234391000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:234373800-234404400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:234375200-234388000	Strong transcription	Lung	lung
14	chr2:234375400-234411200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:234375600-234387400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:234376000-234389400	Weak transcription	NH-A	brain
17	chr2:234376200-234390200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:234377800-234391400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr2:234377800-234397200	Weak transcription	Small Intestine	intestine
20	chr2:234378000-234387000	Weak transcription	HSMM	muscle
21	chr2:234378200-234395000	Weak transcription	Right Atrium	heart
22	chr2:234378400-234388000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:234378400-234390200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:234378400-234390800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:234378400-234391000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr2:234378600-234391600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:234378800-234391400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:234379000-234386600	Weak transcription	HepG2	liver
29	chr2:234379000-234391200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:234379400-234388400	Weak transcription	Stomach Mucosa	stomach
31	chr2:234379600-234386400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr2:234380400-234390200	Weak transcription	HMEC	breast
33	chr2:234380800-234386000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr2:234380800-234395000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:234381200-234394800	Strong transcription	Pancreas	Pancrea
36	chr2:234381400-234389000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:234381600-234391000	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr2:234381600-234393400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr2:234381600-234399600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr2:234381800-234390400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:234382000-234391600	Weak transcription	GM12878-XiMat	blood
42	chr2:234382200-234386400	Weak transcription	Primary B cells from cord blood	blood
43	chr2:234382200-234387600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:234382200-234387800	Strong transcription	Colonic Mucosa	Colon
45	chr2:234382400-234387000	Weak transcription	HSMMtube	muscle
46	chr2:234382800-234388400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:234382800-234388800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:234383000-234386200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr2:234383000-234395000	Strong transcription	NHLF	lung
50	chr2:234383400-234391200	Weak transcription	H1 Cell Line	embryonic stem cell

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