Variant report

Variant	rs838557
Chromosome Location	chr2:234410541-234410542
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	chr2:234398690..234402106-chr2:234407622..234410683,3	MCF-7	breast:
2	chr2:234405752..234408399-chr2:234409710..234413994,3	K562	blood:

Variant related genes	Relation type
ENSG00000085982	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10168794	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10169180	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs10177112	0.94[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs10178062	0.96[EUR][1000 genomes]
rs10178357	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs10181039	0.84[ASN][1000 genomes]
rs10183033	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs10185923	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs10193542	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10198879	0.94[EUR][1000 genomes]
rs10207915	0.98[EUR][1000 genomes]
rs10208361	0.96[EUR][1000 genomes]
rs1037451	0.94[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs10803653	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs10929195	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs10929200	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10929208	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs1097929	0.98[EUR][1000 genomes]
rs1097930	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs1097931	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs11690686	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11892545	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1220430	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs12467878	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs12473743	0.95[EUR][1000 genomes]
rs12473824	0.95[EUR][1000 genomes]
rs12615446	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs12692193	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12692195	0.96[EUR][1000 genomes]
rs13002253	0.96[EUR][1000 genomes]
rs13018364	0.93[EUR][1000 genomes]
rs13384932	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13392183	0.84[ASN][1000 genomes]
rs13400563	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13427703	1.00[CHB][hapmap]
rs1377459	0.96[EUR][1000 genomes]
rs1377461	0.92[EUR][1000 genomes]
rs1453321	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs1470864	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs1470865	0.96[EUR][1000 genomes]
rs1542325	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs1542326	0.95[EUR][1000 genomes]
rs1545524	0.82[EUR][1000 genomes]
rs1545525	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs1597940	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs1901812	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs2034675	0.95[EUR][1000 genomes]
rs2124045	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs2167884	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs2167885	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs2602387	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs2602389	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs2603545	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs2603546	0.98[EUR][1000 genomes]
rs2603547	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs2924809	1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs2924810	1.00[ASN][1000 genomes]
rs2924811	0.88[EUR][1000 genomes]
rs2924813	0.91[EUR][1000 genomes]
rs2971861	0.91[EUR][1000 genomes]
rs2971862	0.93[EUR][1000 genomes]
rs2971863	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs2971864	0.93[EUR][1000 genomes]
rs2971865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2971866	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2971867	0.93[EUR][1000 genomes]
rs2971869	0.89[EUR][1000 genomes]
rs2971870	0.93[EUR][1000 genomes]
rs2971871	0.93[EUR][1000 genomes]
rs2971872	0.93[EUR][1000 genomes]
rs2971873	1.00[ASN][1000 genomes]
rs3792104	1.00[CHB][hapmap]
rs3792105	1.00[CHB][hapmap]
rs4047187	0.96[EUR][1000 genomes]
rs4047188	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4047198	1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs4047199	1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs4233627	0.98[EUR][1000 genomes]
rs4663684	0.96[EUR][1000 genomes]
rs4663698	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs55679565	0.96[EUR][1000 genomes]
rs58685260	1.00[ASN][1000 genomes]
rs59160392	0.86[EUR][1000 genomes]
rs6710645	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs6710772	0.96[EUR][1000 genomes]
rs6716988	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6720619	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs6726184	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6745134	1.00[CHB][hapmap]
rs6753062	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs6756068	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs73115402	0.84[ASN][1000 genomes]
rs73117551	0.84[ASN][1000 genomes]
rs7422734	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7557849	0.98[EUR][1000 genomes]
rs7567713	0.96[EUR][1000 genomes]
rs7571288	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs7572310	0.93[EUR][1000 genomes]
rs7575694	0.93[EUR][1000 genomes]
rs7578898	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs7588509	1.00[CHB][hapmap]
rs7599285	0.98[EUR][1000 genomes]
rs7603410	0.95[EUR][1000 genomes]
rs7604337	0.88[EUR][1000 genomes]
rs7724	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs838543	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs838544	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs838545	0.97[EUR][1000 genomes]
rs838548	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs838549	0.93[CEU][hapmap];0.98[EUR][1000 genomes]
rs838550	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs838551	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs838552	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs838555	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs838558	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes]
rs838559	0.93[EUR][1000 genomes]
rs838561	0.94[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs838562	0.94[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs860794	0.96[EUR][1000 genomes]
rs896833	0.98[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	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
5	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234364000-234411200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:234375400-234411200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:234384000-234412400	Weak transcription	Fetal Heart	heart
4	chr2:234387400-234466000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr2:234390800-234441000	Weak transcription	Fetal Brain Male	brain
6	chr2:234391600-234412000	Strong transcription	Skeletal Muscle Female	skeletal muscle
7	chr2:234392000-234411600	Weak transcription	Fetal Brain Female	brain
8	chr2:234395600-234431800	Weak transcription	Colonic Mucosa	Colon
9	chr2:234395800-234411400	Strong transcription	Liver	Liver
10	chr2:234397800-234411400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr2:234398000-234452800	Weak transcription	HUVEC	blood vessel
12	chr2:234398200-234411200	Weak transcription	Esophagus	oesophagus
13	chr2:234398200-234411200	Weak transcription	Thymus	Thymus
14	chr2:234398400-234442400	Weak transcription	Hela-S3	cervix
15	chr2:234398600-234431800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:234400200-234410600	Weak transcription	Small Intestine	intestine
17	chr2:234400400-234430000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:234401200-234411200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:234401200-234430800	Weak transcription	NHLF	lung
20	chr2:234402200-234410600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:234402200-234411200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:234402200-234411200	Weak transcription	Pancreas	Pancrea
23	chr2:234402200-234411200	Weak transcription	Spleen	Spleen
24	chr2:234402200-234411200	Weak transcription	Dnd41	blood
25	chr2:234402200-234472400	Weak transcription	Psoas Muscle	Psoas
26	chr2:234402600-234429800	Weak transcription	Right Ventricle	heart
27	chr2:234402600-234430600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:234402600-234436800	Weak transcription	Gastric	stomach
29	chr2:234402600-234454000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:234403600-234411200	Strong transcription	Adipose Nuclei	Adipose
31	chr2:234404200-234411200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr2:234404400-234455000	Weak transcription	Fetal Thymus	thymus
33	chr2:234405000-234431200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr2:234406000-234410600	Strong transcription	A549	lung
35	chr2:234406200-234411000	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr2:234406800-234411000	Weak transcription	Fetal Intestine Small	intestine
37	chr2:234406800-234411000	Weak transcription	Lung	lung
38	chr2:234407000-234411000	Weak transcription	Fetal Stomach	stomach
39	chr2:234407000-234411200	Weak transcription	Brain Angular Gyrus	brain
40	chr2:234407000-234411200	Weak transcription	HepG2	liver
41	chr2:234407400-234410800	Weak transcription	Primary B cells from cord blood	blood
42	chr2:234407400-234411200	Weak transcription	HSMMtube	muscle
43	chr2:234407400-234412000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr2:234407400-234412000	Weak transcription	Colon Smooth Muscle	Colon
45	chr2:234407600-234410800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr2:234407600-234411200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:234407600-234419600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr2:234407800-234411200	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr2:234407800-234431800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:234407800-234436800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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