Variant report

Variant	rs2980683
Chromosome Location	chr8:6585879-6585880
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:6585827..6588340-chr8:6594448..6598218,3	K562	blood:
2	chr8:6582711..6584334-chr8:6584335..6586041,2	K562	blood:
3	chr8:6585357..6588723-chr8:6589806..6592858,3	K562	blood:
4	chr8:6585868..6588138-chr8:6590976..6594012,3	K562	blood:
5	chr8:6563956..6568156-chr8:6584449..6592281,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249898	Chromatin interaction
ENSG00000155189	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10096753	0.96[CEU][hapmap]
rs10108451	0.84[CEU][hapmap]
rs10110103	0.92[CEU][hapmap];0.95[GIH][hapmap]
rs1365041	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1365042	1.00[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1365043	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1559744	0.89[CEU][hapmap]
rs1559748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1961768	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1971312	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2059536	0.85[EUR][1000 genomes]
rs2408444	0.92[CEU][hapmap]
rs2911970	0.97[MKK][hapmap]
rs2911975	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2911976	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2911977	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2911978	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2911979	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2911980	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2911982	0.82[EUR][1000 genomes]
rs2911983	0.91[EUR][1000 genomes]
rs2911987	0.84[EUR][1000 genomes]
rs2911992	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2912054	0.92[CEU][hapmap];0.93[GIH][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs2912067	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2912068	0.84[ASN][1000 genomes]
rs2928576	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[GIH][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs2928579	0.97[MKK][hapmap]
rs2928617	0.85[EUR][1000 genomes]
rs2928618	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2928619	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2928621	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2928623	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2928625	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2928626	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2928629	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2928630	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs2928631	0.89[EUR][1000 genomes]
rs2936502	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs2936507	0.83[MKK][hapmap]
rs2936512	1.00[ASW][hapmap];0.88[CEU][hapmap];0.80[GIH][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs2936520	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2980679	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs2980680	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs2980682	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2980684	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2980686	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2980688	0.94[MKK][hapmap]
rs2980689	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs2980690	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2980692	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3780087	0.92[CEU][hapmap];0.89[GIH][hapmap]
rs6559177	0.80[EUR][1000 genomes]
rs6559178	0.86[CEU][hapmap]
rs71505132	0.80[EUR][1000 genomes]
rs992812	0.82[EUR][1000 genomes]
rs992813	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021175	chr8:5965453-6880364	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1027682	chr8:6018123-6920312	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1027313	chr8:6286575-6920312	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1021684	chr8:6350091-6809455	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	esv2422383	chr8:6362389-6781593	Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv610004	chr8:6402366-6772913	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv1029241	chr8:6411300-6761720	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv933075	chr8:6456475-7366650	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
9	nsv1025976	chr8:6472948-6686972	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	nsv933768	chr8:6482944-6618221	Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv831220	chr8:6527845-6728491	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	nsv1030637	chr8:6545498-6669949	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
13	nsv1034115	chr8:6546984-6665832	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
14	nsv465436	chr8:6568201-6921404	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv610006	chr8:6568201-6921404	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	nsv1031063	chr8:6570354-6622685	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
17	nsv1027883	chr8:6570354-7250368	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
18	nsv1024685	chr8:6575334-6622685	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
19	nsv1034812	chr8:6578390-6920312	Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
20	nsv949532	chr8:6579563-6999220	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2980683	MMGT1	trans	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6567400-6586800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr8:6567400-6590000	Weak transcription	Left Ventricle	heart
3	chr8:6567400-6590200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr8:6567400-6590600	Weak transcription	Psoas Muscle	Psoas
5	chr8:6567400-6590800	Weak transcription	Pancreas	Pancrea
6	chr8:6567400-6592600	Weak transcription	Aorta	Aorta
7	chr8:6567600-6586400	Weak transcription	Osteobl	bone
8	chr8:6567600-6589400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr8:6567800-6589200	Weak transcription	Brain Substantia Nigra	brain
10	chr8:6567800-6590000	Weak transcription	NHLF	lung
11	chr8:6568000-6586200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr8:6568000-6589400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr8:6568000-6603400	Weak transcription	Fetal Brain Male	brain
14	chr8:6568400-6589800	Weak transcription	HSMMtube	muscle
15	chr8:6568400-6590400	Weak transcription	Brain Germinal Matrix	brain
16	chr8:6571400-6587200	Weak transcription	Small Intestine	intestine
17	chr8:6572400-6590000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr8:6575800-6586200	Weak transcription	NHEK	skin
19	chr8:6575800-6586400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr8:6576000-6589800	Weak transcription	Fetal Muscle Leg	muscle
21	chr8:6576000-6590800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr8:6576000-6590800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr8:6576000-6591200	Weak transcription	Fetal Stomach	stomach
24	chr8:6576200-6586000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr8:6576200-6589400	Weak transcription	Brain Anterior Caudate	brain
26	chr8:6576200-6590200	Weak transcription	Fetal Heart	heart
27	chr8:6576200-6590400	Weak transcription	Fetal Brain Female	brain
28	chr8:6576400-6586200	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr8:6576400-6588000	Weak transcription	Fetal Thymus	thymus
30	chr8:6576400-6590200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr8:6576600-6586600	Weak transcription	HMEC	breast
32	chr8:6576600-6587000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr8:6577200-6590000	Weak transcription	Thymus	Thymus
34	chr8:6577600-6586000	Weak transcription	HSMM	muscle
35	chr8:6577800-6592000	Weak transcription	Placenta	Placenta
36	chr8:6578200-6589400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr8:6578200-6590600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr8:6578600-6588200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr8:6579200-6586400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr8:6580600-6586200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr8:6581800-6587000	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr8:6582600-6587800	Enhancers	Primary hematopoietic stem cells	blood
43	chr8:6582600-6594600	Strong transcription	Hela-S3	cervix
44	chr8:6582800-6587800	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr8:6583000-6589400	Weak transcription	A549	lung
46	chr8:6583200-6587000	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr8:6583200-6587800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr8:6583400-6586400	Weak transcription	Primary B cells from cord blood	blood
49	chr8:6583400-6587200	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr8:6583400-6589200	Weak transcription	Fetal Kidney	kidney

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