Variant report

Variant	rs11682530
Chromosome Location	chr2:63073194-63073195
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	chr2:63073137..63075941-chr2:63076155..63077726,2	K562	blood:

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1022110	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11688816	1.00[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MKK][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11893131	0.96[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12328837	0.93[JPT][hapmap]
rs12713467	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12713468	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12713469	0.85[CHB][hapmap];0.97[CHD][hapmap]
rs12989754	0.93[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12994674	0.87[ASN][1000 genomes]
rs13013218	0.93[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13398408	0.84[YRI][hapmap]
rs13418889	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1420018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1468748	0.93[ASW][hapmap];0.92[CEU][hapmap];0.84[GIH][hapmap];0.83[LWK][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.89[EUR][1000 genomes]
rs1487074	0.93[JPT][hapmap]
rs1534418	0.93[JPT][hapmap]
rs1534420	0.93[JPT][hapmap]
rs1553832	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17027429	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[GIH][hapmap];0.86[LWK][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1828398	0.92[CEU][hapmap];0.92[YRI][hapmap];0.86[EUR][1000 genomes]
rs1872789	0.93[JPT][hapmap]
rs1872790	0.93[JPT][hapmap]
rs189671	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1906198	0.93[GIH][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap]
rs2058566	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2058567	0.91[EUR][1000 genomes]
rs2080227	0.92[YRI][hapmap];0.91[AFR][1000 genomes]
rs2136737	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2204655	0.93[JPT][hapmap]
rs2204656	0.93[JPT][hapmap]
rs2215870	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2421816	0.96[CEU][hapmap];0.90[GIH][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs2430388	0.86[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2539978	0.96[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs2539980	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2539981	0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2539985	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2539987	0.86[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.83[EUR][1000 genomes]
rs2710637	0.92[CEU][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs2710638	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2710639	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs2710640	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2710642	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2710644	0.80[EUR][1000 genomes]
rs2710647	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs360797	0.93[ASW][hapmap];0.83[CEU][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];0.92[YRI][hapmap]
rs360799	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.83[YRI][hapmap];0.82[ASN][1000 genomes]
rs360800	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[ASN][1000 genomes]
rs360801	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs360804	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs360807	0.93[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.92[YRI][hapmap]
rs360808	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs3927201	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4461246	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4671050	0.86[ASW][hapmap];0.87[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes]
rs4671051	0.85[EUR][1000 genomes]
rs4671448	0.90[CHB][hapmap]
rs4671450	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6545969	0.93[JPT][hapmap]
rs6545971	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6545972	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[GIH][hapmap];0.81[LWK][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6545973	0.96[CEU][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs6705798	0.92[CEU][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs6739804	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap]
rs6757128	0.93[JPT][hapmap]
rs7557501	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[GIH][hapmap];0.86[LWK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7562149	0.93[ASW][hapmap];0.87[CEU][hapmap];0.84[GIH][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap]
rs7562734	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7567923	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[GIH][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7571916	0.91[EUR][1000 genomes]
rs7573756	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9678329	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9789661	0.82[EUR][1000 genomes]
rs9973612	0.87[CEU][hapmap];0.96[YRI][hapmap]

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	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv428041	chr2:63027947-63206574	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1006848	chr2:63061816-63631407	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11682530	VPS54	cis	cerebellum	SCAN
rs11682530	HSPC159	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63020600-63082000	Weak transcription	Pancreas	Pancrea
2	chr2:63031000-63083000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:63031400-63082000	Weak transcription	Thymus	Thymus
4	chr2:63040600-63082000	Weak transcription	Lung	lung
5	chr2:63046400-63101800	Weak transcription	Brain Angular Gyrus	brain
6	chr2:63050600-63091800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:63052000-63099600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:63052200-63098200	Weak transcription	Hela-S3	cervix
9	chr2:63054600-63099800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:63054800-63091600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr2:63055000-63082000	Weak transcription	Esophagus	oesophagus
12	chr2:63056400-63081800	Weak transcription	NHLF	lung
13	chr2:63060800-63081000	Weak transcription	Left Ventricle	heart
14	chr2:63060800-63081800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:63061000-63073200	Weak transcription	NH-A	brain
16	chr2:63061000-63080400	Weak transcription	Aorta	Aorta
17	chr2:63061200-63080800	Weak transcription	Psoas Muscle	Psoas
18	chr2:63061200-63115200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:63061400-63080400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:63061400-63102000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr2:63061600-63082000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:63061800-63073200	Weak transcription	Primary B cells from cord blood	blood
23	chr2:63061800-63080800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:63062000-63076400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:63062000-63080600	Weak transcription	Brain Germinal Matrix	brain
26	chr2:63062000-63081200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:63062000-63082400	Weak transcription	HMEC	breast
28	chr2:63062000-63093000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr2:63062200-63073200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:63062200-63076400	Weak transcription	Osteobl	bone
31	chr2:63062200-63080600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:63062400-63073200	Weak transcription	Fetal Intestine Small	intestine
33	chr2:63063000-63081800	Weak transcription	Fetal Stomach	stomach
34	chr2:63063200-63075800	Weak transcription	Fetal Intestine Large	intestine
35	chr2:63070800-63073200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:63071200-63073400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:63071200-63073400	Strong transcription	Ovary	ovary
38	chr2:63071200-63074000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:63071200-63097200	Strong transcription	HepG2	liver
40	chr2:63071400-63073600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:63071400-63073800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:63071800-63073400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:63071800-63073600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:63071800-63073600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
45	chr2:63071800-63073800	Strong transcription	HSMM	muscle
46	chr2:63072000-63073200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
47	chr2:63072000-63086200	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr2:63072200-63082800	Weak transcription	Primary T cells from cord blood	blood
49	chr2:63072200-63083400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:63072400-63073400	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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