Variant report

Variant	rs10198663
Chromosome Location	chr2:190357442-190357443
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr2:190357276-190357493	IMR90	lung:	n/a	n/a
2	FOS	chr2:190357349-190357491	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr2:190357317-190357517	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:190355063..190357598-chr2:190359651..190361353,2	K562	blood:
2	chr2:190353594..190356120-chr2:190357015..190358667,2	K562	blood:
3	chr2:190348544..190350498-chr2:190356063..190358536,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233996	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10166420	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10175108	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10207812	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs10210634	0.82[ASN][1000 genomes]
rs10931417	0.82[ASN][1000 genomes]
rs11677167	0.82[ASN][1000 genomes]
rs11678414	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12613903	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12622720	1.00[ASN][1000 genomes]
rs12623394	0.93[ASN][1000 genomes]
rs12693539	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12693540	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13009912	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13015207	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13018252	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.83[ASN][1000 genomes]
rs13035381	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1356976	0.83[ASN][1000 genomes]
rs1520854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1520856	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1520858	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1520866	0.94[ASN][1000 genomes]
rs1595749	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];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831454	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1851104	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1866605	0.94[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];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866606	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1898971	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1992295	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2304702	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2351934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2882805	0.83[ASN][1000 genomes]
rs4309611	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4666775	0.94[ASN][1000 genomes]
rs4667280	0.80[ASN][1000 genomes]
rs4667284	0.94[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6434342	0.87[ASN][1000 genomes]
rs6434343	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6738193	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6747222	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6752545	0.82[ASN][1000 genomes]
rs734859	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs744556	0.93[ASN][1000 genomes]
rs745742	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7556928	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7566093	0.82[ASN][1000 genomes]
rs7574403	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8179541	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs8179732	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs893407	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs893408	0.93[ASN][1000 genomes]
rs9677436	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875615	chr2:190215527-190444392	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv584062	chr2:190272195-190376493	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10198663	AC013439.4	cis	Muscle Skeletal	GTEx
rs10198663	PKIG	trans	lymphoblastoid	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190335000-190366200	Weak transcription	Ovary	ovary
2	chr2:190349200-190365000	Weak transcription	Fetal Intestine Large	intestine
3	chr2:190353000-190364600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:190357000-190357600	Enhancers	NH-A	brain
5	chr2:190357000-190357800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:190357000-190358000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:190357200-190358000	Enhancers	HUES6 Cell Line	embryonic stem cell

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