Variant report

Variant	rs6791890
Chromosome Location	chr3:141377022-141377023
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	chr3:141376839..141379290-chr3:141593720..141595646,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000069849	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10935431	0.89[CHD][hapmap];0.85[JPT][hapmap]
rs12632759	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs13088397	0.93[ASN][1000 genomes]
rs13089727	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs13096539	0.80[ASN][1000 genomes]
rs1400685	0.94[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1532247	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1994845	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2640001	0.96[ASN][1000 genomes]
rs2640019	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs295294	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs295296	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs295314	0.91[ASN][1000 genomes]
rs295315	0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs295317	0.93[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs34867571	0.95[ASN][1000 genomes]
rs4467426	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4634089	0.95[ASN][1000 genomes]
rs4683407	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683615	0.86[ASN][1000 genomes]
rs4683616	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59312699	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440024	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6440025	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6768509	0.85[JPT][hapmap]
rs6774986	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6784270	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6784413	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6784623	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6805124	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7618625	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7627285	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7639695	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7642620	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7650428	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7650897	0.81[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs7653258	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs868767	0.83[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs868768	0.83[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs9289635	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9289636	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9289637	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9812758	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9841650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9861838	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv524429	chr3:141372391-141377330	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6791890	GRK7	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141364400-141377600	Weak transcription	Aorta	Aorta
2	chr3:141376000-141377200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:141376200-141378200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:141376400-141377200	Weak transcription	Placenta	Placenta
5	chr3:141376400-141377600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr3:141376400-141377600	Flanking Active TSS	Colon Smooth Muscle	Colon
7	chr3:141376800-141377200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:141376800-141377200	Active TSS	Rectal Smooth Muscle	rectum
9	chr3:141377000-141377800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
10	chr3:141377000-141378400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood

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