Variant report

Variant	rs838549
Chromosome Location	chr2:234433124-234433125
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	chr2:234427830..234430556-chr2:234432658..234434304,2	MCF-7	breast:

Extended variants
information (count: 114 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10169180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10177112	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10178062	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10178357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10183033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10185923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10198879	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10207915	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208361	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1037451	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10803653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10929195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10929200	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10929208	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1097929	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1097930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1097931	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11690686	0.95[EUR][1000 genomes]
rs11888993	0.82[ASN][1000 genomes]
rs11897617	0.85[ASN][1000 genomes]
rs1220430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12467878	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12473743	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12473824	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12615446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12692193	0.98[EUR][1000 genomes]
rs12692195	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13002253	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13018364	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13391864	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs13400471	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs13403169	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs13406655	0.82[JPT][hapmap]
rs13414407	1.00[CHB][hapmap]
rs1377459	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1377461	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1453321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1470864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1470865	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1542325	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1542326	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1545524	0.80[EUR][1000 genomes]
rs1545525	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1597940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1901812	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2034675	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2124045	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2167884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2167885	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2602387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2603545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2603546	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2603547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2924809	0.93[EUR][1000 genomes]
rs2924811	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2924813	0.89[EUR][1000 genomes]
rs2971861	0.93[EUR][1000 genomes]
rs2971862	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2971863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2971864	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2971865	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs2971866	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2971867	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2971869	0.87[EUR][1000 genomes]
rs2971870	0.91[EUR][1000 genomes]
rs2971871	0.91[EUR][1000 genomes]
rs2971872	0.91[EUR][1000 genomes]
rs4047187	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4047188	0.96[EUR][1000 genomes]
rs4047198	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4047199	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4233627	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4663684	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4663698	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55679565	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59160392	0.88[EUR][1000 genomes]
rs6710645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6710772	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6713866	0.81[ASN][1000 genomes]
rs6716988	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6720619	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6726184	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6753062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6756068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7557849	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7567713	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7571288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7572257	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7572310	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7575694	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7578898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7599285	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7603410	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7604337	0.90[EUR][1000 genomes]
rs7724	0.93[EUR][1000 genomes]
rs838543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838545	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838557	0.93[CEU][hapmap];0.98[EUR][1000 genomes]
rs838558	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs838559	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs838561	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs838562	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs860794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs896833	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234387400-234466000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr2:234390800-234441000	Weak transcription	Fetal Brain Male	brain
3	chr2:234398000-234452800	Weak transcription	HUVEC	blood vessel
4	chr2:234398400-234442400	Weak transcription	Hela-S3	cervix
5	chr2:234402200-234472400	Weak transcription	Psoas Muscle	Psoas
6	chr2:234402600-234436800	Weak transcription	Gastric	stomach
7	chr2:234402600-234454000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:234404400-234455000	Weak transcription	Fetal Thymus	thymus
9	chr2:234407800-234436800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:234411600-234465600	Weak transcription	Thymus	Thymus
11	chr2:234412400-234437600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:234412600-234437400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:234413000-234474200	Weak transcription	Fetal Heart	heart
14	chr2:234413200-234440600	Weak transcription	Dnd41	blood
15	chr2:234414000-234461800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:234415400-234440600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:234416200-234441200	Weak transcription	Fetal Kidney	kidney
18	chr2:234416200-234441800	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr2:234418600-234436400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:234423200-234473400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr2:234423600-234439600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:234423800-234441400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:234424600-234433600	Weak transcription	K562	blood
24	chr2:234426200-234474000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:234426400-234453600	Weak transcription	NH-A	brain
26	chr2:234427000-234466200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr2:234427200-234438200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:234427200-234438200	Strong transcription	Liver	Liver
29	chr2:234427200-234438200	Strong transcription	Placenta	Placenta
30	chr2:234427200-234438400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:234427200-234438400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:234427400-234433200	Strong transcription	Stomach Smooth Muscle	stomach
33	chr2:234427400-234434800	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr2:234427400-234435200	Strong transcription	Adipose Nuclei	Adipose
35	chr2:234427400-234438200	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:234427400-234440600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:234427400-234463800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:234427600-234440400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:234428600-234433800	Strong transcription	Fetal Muscle Trunk	muscle
40	chr2:234428600-234440800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr2:234428600-234440800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr2:234428800-234474400	Weak transcription	Brain Germinal Matrix	brain
43	chr2:234429000-234433600	Strong transcription	Osteobl	bone
44	chr2:234429600-234438400	Strong transcription	Fetal Muscle Leg	muscle
45	chr2:234429800-234434600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:234429800-234434600	Strong transcription	Brain Substantia Nigra	brain
47	chr2:234429800-234434800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:234429800-234435200	Strong transcription	A549	lung
49	chr2:234429800-234437800	Strong transcription	Left Ventricle	heart
50	chr2:234429800-234438400	Strong transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links