Variant report

Variant	rs6855482
Chromosome Location	chr4:100056959-100056960
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	chr4:100008381..100011330-chr4:100056699..100058939,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197894	Chromatin interaction
ENSG00000246090	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10014222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10017466	1.00[CHD][hapmap]
rs1126670	1.00[CHD][hapmap]
rs1126671	1.00[CHD][hapmap]
rs1126673	1.00[CHD][hapmap]
rs1229968	0.83[AMR][1000 genomes]
rs1229983	0.83[AMR][1000 genomes]
rs1229985	0.83[AMR][1000 genomes]
rs1229988	0.83[AMR][1000 genomes]
rs1230015	0.83[AMR][1000 genomes]
rs1230017	0.83[AMR][1000 genomes]
rs1230021	0.83[AMR][1000 genomes]
rs1230024	0.83[AMR][1000 genomes]
rs1230029	0.83[AMR][1000 genomes]
rs1235416	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs1540053	1.00[CHD][hapmap]
rs1573495	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17028500	0.94[AMR][1000 genomes]
rs1789875	0.83[AMR][1000 genomes]
rs1789877	0.83[AMR][1000 genomes]
rs1789878	0.83[AMR][1000 genomes]
rs1789879	0.83[AMR][1000 genomes]
rs1789883	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs1893881	1.00[CHD][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1984360	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1984361	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1984365	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2032349	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2156734	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2187482	0.82[AFR][1000 genomes]
rs2213030	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2213031	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2213034	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2602886	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2866039	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2866041	0.83[AMR][1000 genomes]
rs28730582	0.94[AMR][1000 genomes]
rs28730612	0.83[AMR][1000 genomes]
rs29001198	0.95[AFR][1000 genomes]
rs29001345	0.94[AMR][1000 genomes]
rs29001347	0.94[AMR][1000 genomes]
rs2903167	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3018045	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4141887	1.00[CHD][hapmap]
rs4407513	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4502688	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4613578	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4699715	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4699719	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4699723	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6532797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6532798	1.00[CHD][hapmap]
rs6532800	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6532801	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6532807	1.00[CEU][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs6824171	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6836440	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6837685	1.00[CHD][hapmap]
rs6848576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7678936	1.00[CHD][hapmap]
rs7691700	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7697795	0.84[AMR][1000 genomes]
rs9307234	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1005446	chr4:99988287-100121669	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv537196	chr4:99988287-100121669	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1002574	chr4:100023999-100133693	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3528915	chr4:100025155-100096234	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3528916	chr4:100025155-100096234	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6855482	ZNF185	trans	lymphoblastoid	seeQTL
rs6855482	TMPRSS3	trans	lymphoblastoid	seeQTL
rs6855482	RASIP1	trans	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100012800-100063800	Weak transcription	Aorta	Aorta
2	chr4:100035000-100098200	Weak transcription	Ovary	ovary
3	chr4:100039800-100064800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr4:100044400-100063600	Weak transcription	Fetal Intestine Small	intestine
5	chr4:100048800-100063800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr4:100051400-100063600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:100051600-100057000	Weak transcription	HepG2	liver
8	chr4:100054400-100057800	Strong transcription	Duodenum Mucosa	Duodenum
9	chr4:100055000-100057600	Genic enhancers	Liver	Liver
10	chr4:100055200-100057200	Enhancers	Placenta Amnion	Placenta Amnion
11	chr4:100056400-100057000	Enhancers	Placenta	Placenta
12	chr4:100056600-100057200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:100056600-100057800	Strong transcription	Fetal Lung	lung
14	chr4:100056800-100082600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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