Variant report

Variant	rs1531479
Chromosome Location	chr11:10556930-10556931
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:10537500..10540065-chr11:10555082..10557780,2	K562	blood:
2	chr11:10548650..10551746-chr11:10552608..10557430,5	K562	blood:
3	chr11:10429330..10431573-chr11:10556869..10558630,2	K562	blood:

Variant related genes	Relation type
ENSG00000133805	Chromatin interaction
ENSG00000110315	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10219352	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10437597	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10500726	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1062912	0.96[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1065052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1074375	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1074377	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10770123	0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs10840431	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10840435	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840436	0.98[ASN][1000 genomes]
rs10840440	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs10840443	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11042876	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11042877	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11042882	0.91[CEU][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11042883	0.88[CEU][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes]
rs12277871	0.98[ASN][1000 genomes]
rs12279850	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12288969	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1964537	0.96[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1993817	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1993818	0.85[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1993819	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2054392	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2071018	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2288236	0.92[CEU][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34466373	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3741033	0.96[CEU][hapmap]
rs3741037	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs3741038	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs3741039	0.86[ASN][1000 genomes]
rs3741041	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs3781863	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910146	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4910153	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6484344	0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7115310	0.92[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs7118551	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7358373	0.96[CEU][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs746164	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7951653	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv1044011	chr11:10529353-10564450	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1531479	OVCH2	cis	cerebellum	SCAN
rs1531479	CTR9	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10502600-10560800	Weak transcription	Fetal Brain Male	brain
2	chr11:10522400-10560800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:10526400-10561600	Weak transcription	Colonic Mucosa	Colon
4	chr11:10533200-10561600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr11:10533200-10561600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr11:10533400-10561400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr11:10533800-10557400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr11:10538200-10561600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:10538400-10561600	Weak transcription	Esophagus	oesophagus
10	chr11:10538400-10561600	Weak transcription	Lung	lung
11	chr11:10541400-10561600	Weak transcription	Fetal Heart	heart
12	chr11:10541600-10561400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr11:10541600-10562000	Weak transcription	Gastric	stomach
14	chr11:10542200-10561600	Weak transcription	Fetal Stomach	stomach
15	chr11:10544200-10561400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr11:10546800-10561400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr11:10549200-10561600	Weak transcription	Right Ventricle	heart
18	chr11:10549400-10560800	Weak transcription	Aorta	Aorta
19	chr11:10549400-10560800	Weak transcription	HSMMtube	muscle
20	chr11:10549400-10561400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr11:10549400-10562000	Weak transcription	Spleen	Spleen
22	chr11:10549600-10560600	Weak transcription	Hela-S3	cervix
23	chr11:10549600-10561400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr11:10549600-10561400	Weak transcription	Fetal Intestine Small	intestine
25	chr11:10551000-10561600	Weak transcription	Left Ventricle	heart
26	chr11:10551200-10559400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:10551200-10559800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr11:10551200-10561400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr11:10551200-10561400	Weak transcription	Fetal Kidney	kidney
30	chr11:10551200-10561400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr11:10551400-10560200	Weak transcription	A549	lung
32	chr11:10551400-10561400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr11:10551400-10561400	Weak transcription	Fetal Brain Female	brain
34	chr11:10551400-10561400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr11:10551400-10561600	Weak transcription	Placenta	Placenta
36	chr11:10551400-10561800	Weak transcription	Brain Germinal Matrix	brain
37	chr11:10551600-10557600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr11:10551600-10561200	Weak transcription	HMEC	breast
39	chr11:10551600-10561400	Weak transcription	NH-A	brain
40	chr11:10551600-10561600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr11:10551800-10561200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr11:10551800-10561200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr11:10551800-10561600	Weak transcription	Psoas Muscle	Psoas
44	chr11:10551800-10561800	Weak transcription	Ovary	ovary
45	chr11:10552000-10559600	Weak transcription	Brain Angular Gyrus	brain
46	chr11:10552000-10561600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr11:10552200-10557000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr11:10552200-10561000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr11:10552200-10561400	Weak transcription	NHLF	lung
50	chr11:10552200-10561600	Weak transcription	Rectal Smooth Muscle	rectum

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