Variant report

Variant	rs2971865
Chromosome Location	chr2:234388689-234388690
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:234382281..234385759-chr2:234386993..234388960,3	MCF-7	breast:
2	chr2:234377292..234380088-chr2:234386184..234389025,2	MCF-7	breast:
3	chr2:234386983..234399433-chr2:234613282..234621553,23	MCF-7	breast:
4	chr2:234381434..234384275-chr2:234387365..234389292,3	K562	blood:
5	chr2:234387239..234389851-chr2:234760888..234763623,2	MCF-7	breast:
6	chr2:234387565..234390486-chr2:234761608..234763193,2	MCF-7	breast:
7	chr2:234387197..234390730-chr2:234600088..234603557,3	MCF-7	breast:
8	chr2:234356161..234358499-chr2:234388405..234391243,2	MCF-7	breast:
9	chr2:234386214..234389809-chr2:234395089..234397205,3	MCF-7	breast:
10	chr2:234388450..234390817-chr2:234616855..234619470,2	MCF-7	breast:
11	chr2:234386808..234389018-chr2:234473935..234476194,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000085982	Chromatin interaction
ENSG00000077044	Chromatin interaction
ENSG00000123485	Chromatin interaction
ENSG00000167165	Chromatin interaction
ENSG00000224814	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10168794	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10169180	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs10177112	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs10178062	0.91[EUR][1000 genomes]
rs10178357	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs10181039	0.84[ASN][1000 genomes]
rs10183033	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs10185923	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs10193542	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10198879	0.89[EUR][1000 genomes]
rs10199833	1.00[CHB][hapmap]
rs10207915	0.93[EUR][1000 genomes]
rs10208361	0.91[EUR][1000 genomes]
rs1037451	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs10803653	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs10929195	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs10929200	0.90[EUR][1000 genomes]
rs10929208	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs1097929	0.93[EUR][1000 genomes]
rs1097930	0.94[CEU][hapmap];0.95[GIH][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs1097931	0.94[CEU][hapmap];0.95[GIH][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs11690686	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11892545	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap]
rs1220430	0.94[CEU][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs12467878	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs12473743	0.90[EUR][1000 genomes]
rs12473824	0.90[EUR][1000 genomes]
rs12615446	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs12692193	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12692195	0.91[EUR][1000 genomes]
rs13002253	0.91[EUR][1000 genomes]
rs13018364	0.88[EUR][1000 genomes]
rs13384932	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13391864	0.85[LWK][hapmap];0.92[MKK][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	0.91[EUR][1000 genomes]
rs1377461	0.88[EUR][1000 genomes]
rs1453321	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs1470864	0.94[CEU][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs1470865	0.91[EUR][1000 genomes]
rs1542325	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs1542326	0.90[EUR][1000 genomes]
rs1545524	0.82[AMR][1000 genomes]
rs1545525	0.94[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs1597940	0.94[CEU][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs1901812	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs2034675	0.90[EUR][1000 genomes]
rs2124045	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs2167884	0.94[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs2167885	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs2602387	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs2602389	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs2603545	0.94[CEU][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs2603546	0.93[EUR][1000 genomes]
rs2603547	0.94[CEU][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs2924809	1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2924810	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2924811	0.92[EUR][1000 genomes]
rs2924813	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2971861	0.95[EUR][1000 genomes]
rs2971862	0.96[EUR][1000 genomes]
rs2971863	0.94[CEU][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs2971864	0.97[EUR][1000 genomes]
rs2971866	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2971867	0.97[EUR][1000 genomes]
rs2971869	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2971870	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2971871	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2971872	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2971873	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792104	1.00[CHB][hapmap]
rs3792105	1.00[CHB][hapmap]
rs4047187	0.91[EUR][1000 genomes]
rs4047188	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4047198	1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs4047199	1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs4233627	0.93[EUR][1000 genomes]
rs4663684	0.91[EUR][1000 genomes]
rs4663698	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs55679565	0.91[EUR][1000 genomes]
rs58685260	1.00[ASN][1000 genomes]
rs59160392	0.90[EUR][1000 genomes]
rs6710645	0.94[CEU][hapmap];0.95[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs6710772	0.91[EUR][1000 genomes]
rs6716988	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[EUR][1000 genomes]
rs6720619	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs6726184	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs6745134	1.00[CHB][hapmap]
rs6753062	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs6756068	0.94[CEU][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.90[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	0.93[EUR][1000 genomes]
rs7567713	0.91[EUR][1000 genomes]
rs7571288	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs7572310	0.88[EUR][1000 genomes]
rs7575694	0.88[EUR][1000 genomes]
rs7578898	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs7588509	1.00[CHB][hapmap]
rs7599285	0.93[EUR][1000 genomes]
rs7603410	0.90[EUR][1000 genomes]
rs7604337	0.83[EUR][1000 genomes]
rs7724	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs838543	0.94[CEU][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs838544	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs838545	0.92[EUR][1000 genomes]
rs838548	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs838549	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs838550	0.94[CEU][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs838551	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs838552	0.94[CEU][hapmap];0.95[GIH][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs838555	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs838557	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]
rs838558	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs838559	0.97[EUR][1000 genomes]
rs838561	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes]
rs838562	0.94[CEU][hapmap];1.00[CHB][hapmap];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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2971865	DNER	cis	cerebellum	SCAN

Chromatin state (count:121 , 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	chr2:234375400-234411200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:234376000-234389400	Weak transcription	NH-A	brain
15	chr2:234376200-234390200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr2:234377800-234391400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:234377800-234397200	Weak transcription	Small Intestine	intestine
18	chr2:234378200-234395000	Weak transcription	Right Atrium	heart
19	chr2:234378400-234390200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr2:234378400-234390800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:234378400-234391000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr2:234378600-234391600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:234378800-234391400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:234379000-234391200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr2:234380400-234390200	Weak transcription	HMEC	breast
26	chr2:234380800-234395000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:234381200-234394800	Strong transcription	Pancreas	Pancrea
28	chr2:234381400-234389000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:234381600-234391000	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr2:234381600-234393400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr2:234381600-234399600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr2:234381800-234390400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:234382000-234391600	Weak transcription	GM12878-XiMat	blood
34	chr2:234382800-234388800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:234383000-234395000	Strong transcription	NHLF	lung
36	chr2:234383400-234391200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr2:234383400-234391400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:234383400-234395400	Strong transcription	Brain Hippocampus Middle	brain
39	chr2:234383400-234400200	Strong transcription	Fetal Intestine Small	intestine
40	chr2:234384000-234389200	Strong transcription	Stomach Smooth Muscle	stomach
41	chr2:234384000-234392800	Strong transcription	Thymus	Thymus
42	chr2:234384000-234395200	Strong transcription	Liver	Liver
43	chr2:234384000-234412400	Weak transcription	Fetal Heart	heart
44	chr2:234384200-234390200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:234384200-234391600	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:234384200-234392800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:234384200-234394400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:234384200-234394400	Strong transcription	Placenta	Placenta
49	chr2:234384200-234394600	Strong transcription	Fetal Thymus	thymus
50	chr2:234384200-234394800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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