Variant report

Variant	rs6716988
Chromosome Location	chr2:234440393-234440394
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:234430061..234434365-chr2:234434465..234441171,6	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HJURP-9	chr2:234438881-234440744	NONHSAT077496

Variant related genes	Relation type
ENSG00000085982	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10168794	1.00[JPT][hapmap]
rs10169180	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10177112	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178062	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10178357	0.94[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10183033	0.94[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10185923	0.94[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10193542	1.00[JPT][hapmap]
rs10198879	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10207915	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10208361	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1037451	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10803653	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs10929195	0.94[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10929200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929208	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1097929	0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1097930	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs1097931	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs11690686	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11892545	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1220430	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12467878	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12473743	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12473824	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12615446	0.94[CEU][hapmap];1.00[EUR][1000 genomes]
rs12692193	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12692195	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13002253	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13018364	0.97[EUR][1000 genomes]
rs13384932	1.00[JPT][hapmap]
rs13400563	1.00[JPT][hapmap]
rs13427703	1.00[CHB][hapmap]
rs1377459	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1377461	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1453321	0.94[CEU][hapmap];0.99[EUR][1000 genomes]
rs1470864	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs1470865	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1542325	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1542326	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545524	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1545525	0.94[CEU][hapmap];0.99[EUR][1000 genomes]
rs1597940	0.94[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1901812	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2034675	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2124045	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs2167884	0.94[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2167885	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2602387	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2602389	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2603545	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2603546	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2603547	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs2924809	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs2924811	0.89[EUR][1000 genomes]
rs2924813	0.88[EUR][1000 genomes]
rs2971861	0.92[EUR][1000 genomes]
rs2971862	0.93[EUR][1000 genomes]
rs2971863	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs2971864	0.94[EUR][1000 genomes]
rs2971865	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[EUR][1000 genomes]
rs2971866	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2971867	0.94[EUR][1000 genomes]
rs2971869	0.86[EUR][1000 genomes]
rs2971870	0.89[EUR][1000 genomes]
rs2971871	0.89[EUR][1000 genomes]
rs2971872	0.89[EUR][1000 genomes]
rs4047187	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4047188	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4047198	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4047199	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233627	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4663684	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4663698	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55679565	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59160392	0.87[EUR][1000 genomes]
rs6710645	0.94[CEU][hapmap];0.99[EUR][1000 genomes]
rs6710772	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6720619	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726184	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6753062	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs6756068	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7422734	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7557849	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7567713	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7571288	0.94[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7572310	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7575694	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7578898	0.94[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7599285	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7603410	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7604337	0.88[EUR][1000 genomes]
rs7724	0.92[EUR][1000 genomes]
rs838543	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs838544	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs838545	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs838548	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs838549	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs838550	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs838551	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs838552	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs838555	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs838557	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs838558	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs838559	0.94[EUR][1000 genomes]
rs838561	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs838562	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs860794	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs896833	0.99[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	chr2:234402600-234454000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:234404400-234455000	Weak transcription	Fetal Thymus	thymus
8	chr2:234411600-234465600	Weak transcription	Thymus	Thymus
9	chr2:234413000-234474200	Weak transcription	Fetal Heart	heart
10	chr2:234413200-234440600	Weak transcription	Dnd41	blood
11	chr2:234414000-234461800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr2:234415400-234440600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:234416200-234441200	Weak transcription	Fetal Kidney	kidney
14	chr2:234416200-234441800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr2:234423200-234473400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr2:234423800-234441400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:234426200-234474000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:234426400-234453600	Weak transcription	NH-A	brain
19	chr2:234427000-234466200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr2:234427400-234440600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:234427400-234463800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:234427600-234440400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:234428600-234440800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr2:234428600-234440800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:234428800-234474400	Weak transcription	Brain Germinal Matrix	brain
26	chr2:234430200-234473800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:234430400-234440600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr2:234430400-234443600	Weak transcription	GM12878-XiMat	blood
29	chr2:234430400-234453800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:234430800-234472800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:234431200-234440600	Weak transcription	Brain Angular Gyrus	brain
32	chr2:234431600-234441200	Weak transcription	Fetal Brain Female	brain
33	chr2:234431600-234452200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr2:234432000-234440400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:234432000-234467600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:234432200-234440600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr2:234432200-234440800	Weak transcription	NHLF	lung
38	chr2:234432200-234441000	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr2:234432200-234443200	Weak transcription	NHDF-Ad	bronchial
40	chr2:234432200-234444000	Weak transcription	HMEC	breast
41	chr2:234432200-234447400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:234432200-234452000	Weak transcription	Small Intestine	intestine
43	chr2:234432200-234453000	Weak transcription	Fetal Lung	lung
44	chr2:234432200-234454000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr2:234432200-234474800	Weak transcription	Spleen	Spleen
46	chr2:234432600-234440400	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr2:234432600-234440600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:234432600-234440600	Weak transcription	NHEK	skin
49	chr2:234432600-234474400	Weak transcription	Colonic Mucosa	Colon
50	chr2:234432800-234440600	Weak transcription	Esophagus	oesophagus

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