Variant report

Variant	rs1559652
Chromosome Location	chr11:10665878-10665879
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:10665534..10668459-chr11:10683707..10686559,2	K562	blood:
2	chr11:10430604..10432437-chr11:10665017..10667381,2	K562	blood:
3	chr11:10665821..10668759-chr11:10676865..10679050,3	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1035693	0.80[JPT][hapmap]
rs10431031	0.81[ASN][1000 genomes]
rs10770128	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10770129	0.89[CHD][hapmap];0.81[ASN][1000 genomes]
rs10840451	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs10840454	0.94[ASN][1000 genomes]
rs10840455	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10840456	0.89[CHD][hapmap];0.81[ASN][1000 genomes]
rs10840458	0.87[MEX][hapmap]
rs11042904	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs11042909	0.94[ASN][1000 genomes]
rs12295574	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1544863	0.88[ASW][hapmap];0.87[CEU][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2113897	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3993279	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4909943	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4909944	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4910164	0.86[ASN][1000 genomes]
rs7108708	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs7119452	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs7123106	0.83[ASN][1000 genomes]
rs7127014	0.84[ASN][1000 genomes]
rs7935285	0.83[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs7938635	0.94[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs9633862	0.88[ASN][1000 genomes]
rs9633863	0.93[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	nsv832063	chr11:10618485-10785281	ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1559652	GVIN1	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10646000-10679000	Weak transcription	Fetal Lung	lung
2	chr11:10646200-10679200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr11:10646800-10667600	Weak transcription	Right Atrium	heart
4	chr11:10650400-10678600	Weak transcription	Right Ventricle	heart
5	chr11:10651800-10670600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:10652400-10668200	Weak transcription	NHLF	lung
7	chr11:10653200-10668200	Weak transcription	Esophagus	oesophagus
8	chr11:10653600-10669000	Weak transcription	Fetal Intestine Small	intestine
9	chr11:10658800-10676600	Enhancers	Primary B cells from peripheral blood	blood
10	chr11:10659800-10666000	Weak transcription	Ovary	ovary
11	chr11:10660400-10667600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr11:10661200-10673600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr11:10661600-10669000	Weak transcription	NH-A	brain
14	chr11:10661800-10667600	Weak transcription	Left Ventricle	heart
15	chr11:10662000-10667400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr11:10662400-10672000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr11:10663400-10667600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr11:10663600-10670200	Weak transcription	NHDF-Ad	bronchial
19	chr11:10663800-10669000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr11:10664000-10666800	Weak transcription	K562	blood
21	chr11:10664000-10669000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr11:10664200-10666200	Weak transcription	Lung	lung
23	chr11:10664200-10666800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr11:10664200-10667400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr11:10664200-10667600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr11:10664200-10668000	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr11:10664200-10668600	Weak transcription	Fetal Intestine Large	intestine
28	chr11:10664200-10672000	Weak transcription	Fetal Muscle Leg	muscle
29	chr11:10664200-10678800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr11:10664400-10666800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr11:10664400-10667000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr11:10664400-10667400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr11:10664400-10668800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr11:10664400-10675000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr11:10664600-10666400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:10664600-10670600	Weak transcription	Primary B cells from cord blood	blood
37	chr11:10664800-10667200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:10665000-10666400	Weak transcription	Spleen	Spleen
39	chr11:10665000-10667800	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr11:10665000-10668000	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr11:10665000-10668600	Weak transcription	Placenta	Placenta
42	chr11:10665000-10670000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr11:10665200-10667800	Weak transcription	Brain Anterior Caudate	brain
44	chr11:10665400-10666800	Strong transcription	Aorta	Aorta
45	chr11:10665400-10667400	Weak transcription	Colon Smooth Muscle	Colon
46	chr11:10665400-10667600	Weak transcription	Brain Angular Gyrus	brain
47	chr11:10665600-10666400	Strong transcription	Stomach Smooth Muscle	stomach
48	chr11:10665600-10666600	Genic enhancers	Fetal Stomach	stomach
49	chr11:10665600-10667800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr11:10665600-10668200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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