Variant report

Variant	rs195079
Chromosome Location	chr6:119657640-119657641
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:119655373..119657912-chr6:119662239..119664036,2	K562	blood:
2	chr6:119632816..119634470-chr6:119655470..119658092,2	K562	blood:
3	chr6:119652078..119653909-chr6:119655448..119657841,3	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1104741	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11153798	0.81[EUR][1000 genomes]
rs11153802	0.89[EUR][1000 genomes]
rs11153813	0.80[ASN][1000 genomes]
rs11962211	0.86[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12207164	0.81[EUR][1000 genomes]
rs12211868	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1295379	0.80[ASN][1000 genomes]
rs1295386	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1295390	0.80[ASN][1000 genomes]
rs1298630	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1342316	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1408492	0.89[EUR][1000 genomes]
rs1408493	0.87[EUR][1000 genomes]
rs1797064	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs195046	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs195051	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs195062	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs195063	0.95[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs195071	0.87[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs195076	0.90[ASN][1000 genomes]
rs195078	0.81[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs195081	0.95[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs195083	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs195085	0.85[ASN][1000 genomes]
rs195086	0.86[ASN][1000 genomes]
rs195088	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs195091	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2180040	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2299879	0.89[CHB][hapmap]
rs2299881	0.85[ASN][1000 genomes]
rs3778111	0.80[MEX][hapmap];0.84[MKK][hapmap]
rs4945633	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4946409	0.85[ASN][1000 genomes]
rs6569063	0.87[ASN][1000 genomes]
rs6569074	0.88[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6569075	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6921356	0.86[ASN][1000 genomes]
rs6924723	0.84[ASN][1000 genomes]
rs7357048	0.81[EUR][1000 genomes]
rs7765368	0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs7773367	0.86[ASN][1000 genomes]
rs7775421	0.90[GIH][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs9320684	0.89[CEU][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9372527	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9374791	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9398510	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9489627	0.80[EUR][1000 genomes]
rs9489628	0.81[EUR][1000 genomes]
rs9489633	0.87[EUR][1000 genomes]
rs9489654	0.88[ASN][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	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
3	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
4	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
5	esv1802628	chr6:119647135-119678881	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs195079	GPRC6A	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119625200-119668600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:119627800-119667000	Weak transcription	Gastric	stomach
3	chr6:119636000-119661600	Weak transcription	Colonic Mucosa	Colon
4	chr6:119636200-119661600	Weak transcription	NHDF-Ad	bronchial
5	chr6:119636200-119662000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr6:119636200-119667400	Weak transcription	Right Ventricle	heart
7	chr6:119636200-119667800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:119641400-119668200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr6:119644200-119667000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr6:119644600-119661800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr6:119644800-119661400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr6:119645000-119659600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr6:119645000-119668200	Weak transcription	Aorta	Aorta
14	chr6:119645200-119661800	Weak transcription	Fetal Kidney	kidney
15	chr6:119647600-119662200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:119647600-119664400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr6:119647800-119661400	Weak transcription	Spleen	Spleen
18	chr6:119648200-119661400	Weak transcription	Lung	lung
19	chr6:119648200-119668000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:119648200-119668000	Weak transcription	Esophagus	oesophagus
21	chr6:119648600-119661000	Weak transcription	Fetal Muscle Leg	muscle
22	chr6:119649600-119659800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:119651000-119661600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr6:119651000-119662400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr6:119651000-119667400	Weak transcription	Fetal Stomach	stomach
26	chr6:119651200-119662400	Weak transcription	Placenta	Placenta
27	chr6:119651400-119661200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:119651800-119661600	Weak transcription	Fetal Intestine Large	intestine
29	chr6:119652200-119661400	Weak transcription	Right Atrium	heart
30	chr6:119652200-119667600	Weak transcription	Thymus	Thymus
31	chr6:119652200-119667600	Weak transcription	NHLF	lung
32	chr6:119653200-119658400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr6:119653200-119658400	Weak transcription	Small Intestine	intestine
34	chr6:119653200-119660000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:119653200-119660800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr6:119653200-119661000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:119653200-119661200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr6:119653200-119661200	Weak transcription	Pancreas	Pancrea
39	chr6:119653200-119661400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr6:119653200-119661400	Weak transcription	Fetal Thymus	thymus
41	chr6:119653200-119661400	Weak transcription	Left Ventricle	heart
42	chr6:119653200-119661600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:119653200-119661600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:119653200-119661800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr6:119653200-119667600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:119653200-119667800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr6:119653400-119658200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr6:119653400-119658400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr6:119653400-119661400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:119653400-119662000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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