Variant report

Variant	rs12301980
Chromosome Location	chr12:85411024-85411025
allele	C/T
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	BRCA1	chr12:85410802-85412343	Hela-S3	cervix:	n/a	n/a
2	CEBPB	chr12:85410188-85413247	Hela-S3	cervix:	n/a	chr12:85410652-85410663 chr12:85410652-85410663 chr12:85410652-85410665 chr12:85410434-85410445
3	TCF7L2	chr12:85410786-85411422	Hela-S3	cervix:	n/a	n/a
4	JUND	chr12:85410147-85412349	Hela-S3	cervix:	n/a	chr12:85410392-85410403
5	POLR2A	chr12:85410755-85411036	Hela-S3	cervix:	n/a	n/a
6	MAFK	chr12:85410262-85411266	Hela-S3	cervix:	n/a	n/a
7	EP300	chr12:85410923-85412447	Hela-S3	cervix:	n/a	n/a
8	STAT3	chr12:85410828-85412476	Hela-S3	cervix:	n/a	chr12:85410994-85411008 chr12:85411839-85411850 chr12:85412220-85412231 chr12:85412112-85412126
9	POLR2A	chr12:85410736-85411080	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
TSPAN19	TF binding region

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10160886	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1031190	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10506911	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10506912	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10779148	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10862955	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11116686	0.84[ASN][1000 genomes]
rs11116701	0.97[ASN][1000 genomes]
rs11116702	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11116704	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11116707	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11116708	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11116712	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11532387	0.95[ASN][1000 genomes]
rs11609088	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11612309	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs12227853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12227986	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs12229124	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12229923	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12231122	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs12304556	0.94[EUR][1000 genomes]
rs12814669	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs12817187	0.91[ASN][1000 genomes]
rs13377881	0.80[YRI][hapmap]
rs1389798	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1404867	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1404868	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1404871	0.85[EUR][1000 genomes]
rs1494500	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1494501	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1525548	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168613	0.95[CEU][hapmap]
rs168615	0.88[EUR][1000 genomes]
rs1690835	0.91[EUR][1000 genomes]
rs17012522	0.99[ASN][1000 genomes]
rs17012533	0.86[JPT][hapmap]
rs1838671	0.99[ASN][1000 genomes]
rs1852148	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1973816	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976270	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2048123	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2056638	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2174754	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2305102	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2404772	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2404773	0.84[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs2660449	0.85[EUR][1000 genomes]
rs2660454	0.84[EUR][1000 genomes]
rs2660455	0.84[EUR][1000 genomes]
rs2660459	0.83[EUR][1000 genomes]
rs2708496	0.85[EUR][1000 genomes]
rs2708498	0.84[EUR][1000 genomes]
rs359992	1.00[CEU][hapmap]
rs3765044	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4761074	0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4761075	0.84[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4761077	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4761113	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4761114	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4761115	0.97[ASN][1000 genomes]
rs6539879	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6539881	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs66617212	0.99[ASN][1000 genomes]
rs7132596	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7133493	0.97[ASN][1000 genomes]
rs7133817	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7135053	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs718553	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7302312	0.83[EUR][1000 genomes]
rs7302315	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7304576	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7312075	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7316900	0.96[EUR][1000 genomes]
rs7954110	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956568	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7962411	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962577	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs7965562	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs796567	0.96[CEU][hapmap]
rs7974418	1.00[CEU][hapmap]
rs7974623	0.92[CHB][hapmap];1.00[JPT][hapmap]

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	nsv899377	chr12:85157346-85629241	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1040452	chr12:85179586-85747907	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	esv1792335	chr12:85321249-86003609	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:85408600-85418000	Enhancers	Hela-S3	cervix
2	chr12:85409000-85412200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr12:85409400-85411400	Enhancers	HMEC	breast
4	chr12:85409800-85411200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:85409800-85411400	Enhancers	NHDF-Ad	bronchial
6	chr12:85409800-85411400	Enhancers	NHEK	skin
7	chr12:85409800-85412000	Enhancers	Muscle Satellite Cultured Cells	--
8	chr12:85410200-85411200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:85410200-85412000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:85410600-85411600	Enhancers	HSMM	muscle

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