Variant report

Variant	rs6569063
Chromosome Location	chr6:119596948-119596949
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	chr6:119585220..119587892-chr6:119594736..119597108,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1076656	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1104741	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11153798	0.86[ASN][1000 genomes]
rs11153801	0.80[ASN][1000 genomes]
rs11153802	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11755686	0.80[ASN][1000 genomes]
rs11962211	0.86[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12207164	0.86[ASN][1000 genomes]
rs12211868	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1295386	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1408491	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1408492	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1408493	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1797064	0.84[JPT][hapmap]
rs195046	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs195051	0.98[ASN][1000 genomes]
rs195062	0.87[ASN][1000 genomes]
rs195063	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs195071	0.81[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs195078	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs195079	0.87[ASN][1000 genomes]
rs195081	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs195083	0.87[ASN][1000 genomes]
rs195088	0.98[ASN][1000 genomes]
rs195091	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2064160	0.85[ASN][1000 genomes]
rs2142885	0.96[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2142890	0.86[ASN][1000 genomes]
rs2267672	0.85[ASN][1000 genomes]
rs2299879	0.89[CHB][hapmap]
rs2299881	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299884	0.96[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2357375	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3798609	0.85[ASN][1000 genomes]
rs4945633	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4945634	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6569060	1.00[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6569061	1.00[CEU][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6569074	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6569075	0.81[ASN][1000 genomes]
rs6922115	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6922274	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7357048	0.86[ASN][1000 genomes]
rs7775421	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9320684	0.82[CEU][hapmap];0.98[ASN][1000 genomes]
rs9385068	0.85[ASN][1000 genomes]
rs9401135	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9489624	0.87[EUR][1000 genomes]
rs9489625	0.85[ASN][1000 genomes]
rs9489627	0.86[ASN][1000 genomes]
rs9489628	0.86[ASN][1000 genomes]
rs9489633	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9489637	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9489654	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs980818	1.00[CEU][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs998194	1.00[CEU][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	esv2507819	chr6:119595970-119597506	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6569063	GPRC6A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119558800-119602000	Weak transcription	Gastric	stomach
2	chr6:119589200-119598600	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:119589200-119611000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:119590600-119621800	Weak transcription	Placenta	Placenta
5	chr6:119590800-119617400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:119590800-119626600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:119591000-119599800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:119591000-119599800	Weak transcription	Lung	lung
9	chr6:119591000-119600600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr6:119591000-119624200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:119591200-119602000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:119591200-119604600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:119591400-119601400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:119591800-119597000	Weak transcription	Fetal Kidney	kidney
15	chr6:119592000-119602200	Weak transcription	Left Ventricle	heart
16	chr6:119592000-119604200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:119592200-119597400	Weak transcription	NHLF	lung
18	chr6:119592200-119622200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:119592400-119597200	Weak transcription	Liver	Liver
20	chr6:119592400-119601200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr6:119592400-119604800	Weak transcription	Fetal Intestine Large	intestine
22	chr6:119592400-119610600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:119592400-119620800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr6:119592400-119633600	Weak transcription	Primary T cells from cord blood	blood
25	chr6:119592600-119622200	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr6:119592600-119627200	Weak transcription	Dnd41	blood
27	chr6:119593000-119599800	Weak transcription	Aorta	Aorta
28	chr6:119593000-119622200	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr6:119593000-119624800	Weak transcription	Fetal Thymus	thymus
30	chr6:119593000-119626800	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr6:119593200-119604600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:119593800-119597000	Weak transcription	Primary B cells from cord blood	blood
33	chr6:119594200-119605000	Strong transcription	HepG2	liver
34	chr6:119594600-119598600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:119594800-119597000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:119595000-119597200	Weak transcription	Fetal Lung	lung
37	chr6:119595400-119601600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:119595600-119597200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr6:119595600-119597600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:119596000-119597000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:119596000-119597000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:119596000-119597000	Weak transcription	K562	blood
43	chr6:119596000-119597000	Weak transcription	NHDF-Ad	bronchial
44	chr6:119596400-119597200	Weak transcription	GM12878-XiMat	blood
45	chr6:119596600-119597800	Strong transcription	Primary hematopoietic stem cells	blood
46	chr6:119596800-119597200	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr6:119596800-119597600	Genic enhancers	Adipose Nuclei	Adipose
48	chr6:119596800-119597800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr6:119596800-119597800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr6:119596800-119598600	Weak transcription	Fetal Intestine Small	intestine

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