Variant report

Variant	rs2971871
Chromosome Location	chr2:234379086-234379087
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234370710..234373600-chr2:234378038..234379575,2	MCF-7	breast:
2	chr2:234377919..234380691-chr2:234381184..234384244,3	MCF-7	breast:
3	chr2:234377292..234380088-chr2:234386184..234389025,2	MCF-7	breast:
4	chr2:234378390..234380701-chr2:234395637..234398303,2	K562	blood:
5	chr2:234378675..234382523-chr2:234390792..234394362,4	K562	blood:
6	chr2:234377166..234379474-chr2:234382800..234384518,2	K562	blood:
7	chr2:234377261..234380113-chr2:234384331..234386065,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000077044	Chromatin interaction
ENSG00000085982	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10169180	0.88[EUR][1000 genomes]
rs10177112	0.89[EUR][1000 genomes]
rs10178062	0.89[EUR][1000 genomes]
rs10178357	0.89[EUR][1000 genomes]
rs10183033	0.89[EUR][1000 genomes]
rs10185923	0.89[EUR][1000 genomes]
rs10198879	0.87[EUR][1000 genomes]
rs10207915	0.91[EUR][1000 genomes]
rs10208361	0.89[EUR][1000 genomes]
rs1037451	0.89[EUR][1000 genomes]
rs10803653	0.88[EUR][1000 genomes]
rs10929195	0.89[EUR][1000 genomes]
rs10929200	0.88[EUR][1000 genomes]
rs10929208	0.89[EUR][1000 genomes]
rs1097929	0.91[EUR][1000 genomes]
rs1097930	0.90[EUR][1000 genomes]
rs1097931	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11690686	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11897617	0.80[ASN][1000 genomes]
rs1220430	0.91[EUR][1000 genomes]
rs12467878	0.89[EUR][1000 genomes]
rs12473743	0.89[EUR][1000 genomes]
rs12473824	0.89[EUR][1000 genomes]
rs12615446	0.89[EUR][1000 genomes]
rs12692193	0.93[EUR][1000 genomes]
rs12692195	0.89[EUR][1000 genomes]
rs13002253	0.89[EUR][1000 genomes]
rs13018364	0.88[EUR][1000 genomes]
rs13391864	0.98[ASN][1000 genomes]
rs13393578	0.98[ASN][1000 genomes]
rs1377459	0.89[EUR][1000 genomes]
rs1377461	0.88[EUR][1000 genomes]
rs1453321	0.88[EUR][1000 genomes]
rs1470864	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1470865	0.88[EUR][1000 genomes]
rs1542325	0.89[EUR][1000 genomes]
rs1542326	0.89[EUR][1000 genomes]
rs1545525	0.88[EUR][1000 genomes]
rs1597940	0.89[EUR][1000 genomes]
rs1901812	0.89[EUR][1000 genomes]
rs2034675	0.89[EUR][1000 genomes]
rs2124045	0.95[EUR][1000 genomes]
rs2167884	0.89[EUR][1000 genomes]
rs2167885	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2305541	0.93[ASN][1000 genomes]
rs2602387	0.91[EUR][1000 genomes]
rs2602389	0.91[EUR][1000 genomes]
rs2603545	0.91[EUR][1000 genomes]
rs2603546	0.91[EUR][1000 genomes]
rs2603547	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28588417	0.98[ASN][1000 genomes]
rs2924809	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2924810	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2924811	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2924813	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2971861	0.93[EUR][1000 genomes]
rs2971862	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2971863	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2971864	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2971865	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2971866	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2971867	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2971869	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2971870	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2971872	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2971873	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4047187	0.88[EUR][1000 genomes]
rs4047188	0.91[EUR][1000 genomes]
rs4047198	0.89[EUR][1000 genomes]
rs4047199	0.89[EUR][1000 genomes]
rs4233627	0.91[EUR][1000 genomes]
rs4663684	0.89[EUR][1000 genomes]
rs4663698	0.89[EUR][1000 genomes]
rs55679565	0.89[EUR][1000 genomes]
rs59160392	0.93[EUR][1000 genomes]
rs59458664	0.91[ASN][1000 genomes]
rs6710645	0.88[EUR][1000 genomes]
rs6710772	0.89[EUR][1000 genomes]
rs6716988	0.89[EUR][1000 genomes]
rs6720619	0.88[EUR][1000 genomes]
rs6726184	0.88[EUR][1000 genomes]
rs6753062	0.88[EUR][1000 genomes]
rs6756068	0.89[EUR][1000 genomes]
rs73117559	0.96[ASN][1000 genomes]
rs7557849	0.91[EUR][1000 genomes]
rs7567713	0.89[EUR][1000 genomes]
rs7571288	0.89[EUR][1000 genomes]
rs7572310	0.86[EUR][1000 genomes]
rs7575694	0.86[EUR][1000 genomes]
rs7578898	0.89[EUR][1000 genomes]
rs7599285	0.91[EUR][1000 genomes]
rs7603410	0.89[EUR][1000 genomes]
rs7604337	0.81[EUR][1000 genomes]
rs7724	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs838543	0.91[EUR][1000 genomes]
rs838544	0.90[EUR][1000 genomes]
rs838545	0.90[EUR][1000 genomes]
rs838548	0.91[EUR][1000 genomes]
rs838549	0.91[EUR][1000 genomes]
rs838550	0.91[EUR][1000 genomes]
rs838551	0.90[EUR][1000 genomes]
rs838552	0.90[EUR][1000 genomes]
rs838555	0.91[EUR][1000 genomes]
rs838557	0.93[EUR][1000 genomes]
rs838558	0.91[EUR][1000 genomes]
rs838559	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs838561	0.95[EUR][1000 genomes]
rs838562	0.93[EUR][1000 genomes]
rs860794	0.89[EUR][1000 genomes]
rs896833	0.91[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	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

No data

Chromatin state (count:125 , 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	chr2:234343200-234383000	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:234344000-234382000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:234344200-234382000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:234344200-234382200	Strong transcription	Primary B cells from cord blood	blood
9	chr2:234344200-234382600	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr2:234344400-234381600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:234352400-234380800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:234352400-234382000	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr2:234352600-234380800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:234352600-234380800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:234352600-234381400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:234352600-234381600	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr2:234352600-234381800	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr2:234352600-234382600	Strong transcription	Primary B cells from peripheral blood	blood
19	chr2:234352600-234382600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr2:234352800-234382000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr2:234353400-234379600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr2:234353400-234381600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:234353600-234381800	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr2:234354000-234381600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:234357600-234382000	Strong transcription	Liver	Liver
26	chr2:234358200-234379400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:234361200-234389800	Weak transcription	Fetal Kidney	kidney
28	chr2:234362400-234384600	Strong transcription	Spleen	Spleen
29	chr2:234362600-234379600	Strong transcription	HSMMtube	muscle
30	chr2:234363600-234379800	Weak transcription	HMEC	breast
31	chr2:234363800-234390600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:234364000-234411200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:234365800-234393600	Weak transcription	Hela-S3	cervix
34	chr2:234369200-234381400	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:234370000-234381600	Strong transcription	Fetal Thymus	thymus
36	chr2:234370000-234382000	Strong transcription	Thymus	Thymus
37	chr2:234370200-234381400	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr2:234373000-234392200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr2:234373000-234409800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:234373200-234380200	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr2:234373200-234382800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr2:234373400-234391000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:234373800-234384200	Weak transcription	Osteobl	bone
44	chr2:234373800-234404400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr2:234374600-234380200	Strong transcription	Dnd41	blood
46	chr2:234374800-234379400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:234375000-234379200	Strong transcription	GM12878-XiMat	blood
48	chr2:234375000-234381400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:234375200-234379400	Strong transcription	NHEK	skin
50	chr2:234375200-234380000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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