Variant report

Variant	rs6542839
Chromosome Location	chr2:99464530-99464531
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99461401..99464766-chr2:99483724..99486615,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196872	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10169003	0.87[EUR][1000 genomes]
rs10172158	0.84[EUR][1000 genomes]
rs10181972	0.87[EUR][1000 genomes]
rs10188156	0.93[EUR][1000 genomes]
rs11123755	0.84[EUR][1000 genomes]
rs11887536	0.84[EUR][1000 genomes]
rs11893888	0.89[EUR][1000 genomes]
rs11900176	0.86[MEX][hapmap];0.83[MKK][hapmap]
rs12468024	0.84[EUR][1000 genomes]
rs12712033	0.86[CHB][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes]
rs12712034	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[ASN][1000 genomes]
rs12712035	0.95[CEU][hapmap];0.89[CHB][hapmap];0.92[EUR][1000 genomes]
rs12712036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12712037	0.86[MEX][hapmap]
rs12712038	0.84[EUR][1000 genomes]
rs12712039	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13004923	0.87[EUR][1000 genomes]
rs1356424	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs1568213	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1581250	0.87[EUR][1000 genomes]
rs1581251	0.84[EUR][1000 genomes]
rs1878585	0.87[EUR][1000 genomes]
rs1983352	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs2008648	0.88[AMR][1000 genomes]
rs2138082	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2280142	0.81[MEX][hapmap]
rs2280256	0.84[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs4263159	0.96[CEU][hapmap];0.80[CHB][hapmap];0.93[EUR][1000 genomes]
rs4850888	0.92[EUR][1000 genomes]
rs4851162	0.93[EUR][1000 genomes]
rs4851163	0.93[EUR][1000 genomes]
rs4851167	0.84[EUR][1000 genomes]
rs4851170	0.84[EUR][1000 genomes]
rs4851171	0.84[EUR][1000 genomes]
rs6542837	0.81[MEX][hapmap]
rs6542838	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[EUR][1000 genomes]
rs6711022	0.89[EUR][1000 genomes]
rs6713991	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6714243	0.84[EUR][1000 genomes]
rs6717372	0.82[EUR][1000 genomes]
rs6719634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726156	0.88[EUR][1000 genomes]
rs6757098	0.83[GIH][hapmap]
rs6757099	0.83[EUR][1000 genomes]
rs6760065	0.83[GIH][hapmap]
rs7579189	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[EUR][1000 genomes]
rs7608889	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs981601	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[EUR][1000 genomes]
rs981602	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.91[TSI][hapmap];0.92[EUR][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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582517	chr2:99440917-99487972	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6542839	TEKT4	cis	parietal	SCAN
rs6542839	FER1L5	cis	cerebellum	SCAN
rs6542839	C2orf15	cis	parietal	SCAN
rs6542839	TSGA10	cis	multi-tissue	Pritchard
rs6542839	FAHD2B	cis	parietal	SCAN
rs6542839	TSGA10	cis	cerebellum	SCAN
rs6542839	LIPT1	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99450000-99468400	Weak transcription	Fetal Intestine Small	intestine
2	chr2:99453200-99473200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:99456200-99473000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:99461600-99464800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:99462400-99464800	Enhancers	NHDF-Ad	bronchial
6	chr2:99462400-99465000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:99463400-99465600	Weak transcription	Pancreas	Pancrea
8	chr2:99463400-99485400	Weak transcription	Gastric	stomach
9	chr2:99463800-99465000	Enhancers	Muscle Satellite Cultured Cells	--

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