Variant report

Variant	rs11962211
Chromosome Location	chr6:119591307-119591308
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr6:119590937-119592425	K562	blood:	n/a	n/a
2	POLR2A	chr6:119587881-119591744	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:119590898..119593723-chr6:119598543..119602207,4	K562	blood:
2	chr6:119590898..119592984-chr6:119600707..119602898,2	K562	blood:

Variant related genes	Relation type
ENSG00000216316	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1076656	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1104741	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153798	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11153801	0.81[ASN][1000 genomes]
rs11153802	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11755686	0.81[ASN][1000 genomes]
rs12207164	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12211868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1295386	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1408491	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1408492	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1408493	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1555683	0.81[ASN][1000 genomes]
rs1797064	0.84[JPT][hapmap]
rs195046	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs195051	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs195062	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs195063	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs195071	0.95[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs195078	1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs195079	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs195081	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs195083	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs195088	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs195091	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs195092	0.80[MEX][hapmap];0.84[MKK][hapmap]
rs2064160	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2093906	0.84[AMR][1000 genomes]
rs2142885	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2142890	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2267672	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2299879	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs2299881	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299884	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2357162	0.90[EUR][1000 genomes]
rs2357375	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3798609	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3822997	0.90[EUR][1000 genomes]
rs4945633	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4945634	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4946406	0.87[YRI][hapmap]
rs6569060	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs6569061	0.91[CEU][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes]
rs6569063	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6569074	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6922115	0.80[AMR][1000 genomes]
rs6922274	0.80[AMR][1000 genomes]
rs6933914	0.87[EUR][1000 genomes]
rs7357047	0.90[EUR][1000 genomes]
rs7357048	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7775421	0.82[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9320684	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9385068	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9401135	0.81[AMR][1000 genomes]
rs9489625	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9489627	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9489628	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9489633	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9489637	0.83[EUR][1000 genomes]
rs9489654	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs980818	0.82[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs998194	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv886570	chr6:119450888-119600556	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1017507	chr6:119465981-119664949	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11962211	GPRC6A	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119558800-119602000	Weak transcription	Gastric	stomach
2	chr6:119568600-119592600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr6:119569200-119591600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:119569200-119591600	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr6:119569400-119591600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:119582800-119591600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr6:119583400-119591600	Weak transcription	NHDF-Ad	bronchial
8	chr6:119587200-119591800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr6:119588200-119592000	Strong transcription	Liver	Liver
10	chr6:119589000-119591400	Weak transcription	Fetal Brain Female	brain
11	chr6:119589000-119591600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr6:119589000-119591600	Weak transcription	Fetal Kidney	kidney
13	chr6:119589200-119591600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:119589200-119591600	Weak transcription	Fetal Lung	lung
15	chr6:119589200-119598600	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:119589200-119611000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr6:119589400-119591600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:119589800-119591600	Weak transcription	Primary T cells from cord blood	blood
19	chr6:119590000-119591400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:119590000-119591600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr6:119590000-119591600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:119590200-119591600	Strong transcription	Primary B cells from cord blood	blood
23	chr6:119590200-119591600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:119590400-119591600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:119590400-119591600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:119590600-119591400	Strong transcription	Primary hematopoietic stem cells	blood
27	chr6:119590600-119591400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:119590600-119591600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr6:119590600-119591800	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr6:119590600-119621800	Weak transcription	Placenta	Placenta
31	chr6:119590800-119591600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:119590800-119591600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:119590800-119591800	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr6:119590800-119591800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr6:119590800-119591800	Weak transcription	Ovary	ovary
36	chr6:119590800-119617400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr6:119590800-119626600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr6:119591000-119591400	Weak transcription	Fetal Intestine Large	intestine
39	chr6:119591000-119591600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:119591000-119591600	Weak transcription	Fetal Intestine Small	intestine
41	chr6:119591000-119591600	Weak transcription	Left Ventricle	heart
42	chr6:119591000-119591600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr6:119591000-119591600	Strong transcription	K562	blood
44	chr6:119591000-119591800	ZNF genes & repeats	Thymus	Thymus
45	chr6:119591000-119592000	Strong transcription	HepG2	liver
46	chr6:119591000-119599800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:119591000-119599800	Weak transcription	Lung	lung
48	chr6:119591000-119600600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr6:119591000-119624200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:119591200-119591600	Weak transcription	Adipose Nuclei	Adipose

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