Variant report

Variant	rs195078
Chromosome Location	chr6:119656946-119656947
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:119637199..119643416-chr6:119653635..119657585,6	K562	blood:
2	chr6:119639797..119643416-chr6:119654591..119657389,3	K562	blood:
3	chr6:119654968..119657111-chr6:119667973..119671040,4	MCF-7	breast:
4	chr6:119655373..119657912-chr6:119662239..119664036,2	K562	blood:
5	chr6:119632816..119634470-chr6:119655470..119658092,2	K562	blood:
6	chr6:119652078..119653909-chr6:119655448..119657841,3	K562	blood:

Variant related genes	Relation type
ENSG00000111885	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1076656	0.88[EUR][1000 genomes]
rs1104741	0.85[ASN][1000 genomes]
rs11153813	0.80[ASN][1000 genomes]
rs11962211	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]
rs12211868	0.85[ASN][1000 genomes]
rs1295379	0.80[ASN][1000 genomes]
rs1295386	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1295390	0.80[ASN][1000 genomes]
rs1408491	0.83[EUR][1000 genomes]
rs1797064	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs195046	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs195051	0.88[ASN][1000 genomes]
rs195062	0.83[AMR][1000 genomes];0.80[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	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs195076	0.90[ASN][1000 genomes]
rs195079	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	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs195085	0.85[ASN][1000 genomes]
rs195086	0.86[ASN][1000 genomes]
rs195088	0.88[ASN][1000 genomes]
rs195091	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2142885	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs2299879	0.89[CHB][hapmap]
rs2299881	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2299884	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs2357375	0.86[EUR][1000 genomes]
rs4945633	0.87[ASN][1000 genomes]
rs4945634	0.86[EUR][1000 genomes]
rs4946409	0.85[ASN][1000 genomes]
rs6569060	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs6569061	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs6569063	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6569074	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6569075	0.93[ASN][1000 genomes]
rs6921356	0.86[ASN][1000 genomes]
rs6922115	0.88[EUR][1000 genomes]
rs6922274	0.88[EUR][1000 genomes]
rs6924723	0.84[ASN][1000 genomes]
rs7765368	0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs7773367	0.86[ASN][1000 genomes]
rs7775421	0.88[CEU][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs9320684	0.87[ASN][1000 genomes]
rs9401135	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9489637	0.86[EUR][1000 genomes]
rs9489654	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs980818	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs998194	0.92[CEU][hapmap];0.85[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	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
rs195078	GPRC6A	cis	cerebellum	SCAN

Chromatin state (count:86 , 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	chr6:119648200-119657000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:119648200-119661400	Weak transcription	Lung	lung
20	chr6:119648200-119668000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:119648200-119668000	Weak transcription	Esophagus	oesophagus
22	chr6:119648600-119661000	Weak transcription	Fetal Muscle Leg	muscle
23	chr6:119649600-119659800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:119651000-119661600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr6:119651000-119662400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr6:119651000-119667400	Weak transcription	Fetal Stomach	stomach
27	chr6:119651200-119662400	Weak transcription	Placenta	Placenta
28	chr6:119651400-119661200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr6:119651800-119661600	Weak transcription	Fetal Intestine Large	intestine
30	chr6:119652200-119661400	Weak transcription	Right Atrium	heart
31	chr6:119652200-119667600	Weak transcription	Thymus	Thymus
32	chr6:119652200-119667600	Weak transcription	NHLF	lung
33	chr6:119653200-119657400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:119653200-119658400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr6:119653200-119658400	Weak transcription	Small Intestine	intestine
36	chr6:119653200-119660000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:119653200-119660800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr6:119653200-119661000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:119653200-119661200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr6:119653200-119661200	Weak transcription	Pancreas	Pancrea
41	chr6:119653200-119661400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:119653200-119661400	Weak transcription	Fetal Thymus	thymus
43	chr6:119653200-119661400	Weak transcription	Left Ventricle	heart
44	chr6:119653200-119661600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr6:119653200-119661600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:119653200-119661800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr6:119653200-119667600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:119653200-119667800	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr6:119653400-119657000	Weak transcription	GM12878-XiMat	blood
50	chr6:119653400-119657600	Weak transcription	NHEK	skin

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