Variant report

Variant	rs12634006
Chromosome Location	chr3:161083709-161083710
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:161040142..161042354-chr3:161082440..161084651,2	MCF-7	breast:
2	chr3:160934982..160947568-chr3:161079696..161093037,40	MCF-7	breast:
3	chr3:160936365..160960187-chr3:161078472..161094658,51	MCF-7	breast:
4	chr3:160813033..160824577-chr3:161083489..161092050,35	MCF-7	breast:
5	chr2:178075634..178077444-chr3:161081913..161083742,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169255	Chromatin interaction
ENSG00000170144	Chromatin interaction
ENSG00000169251	Chromatin interaction
ENSG00000229337	Chromatin interaction
ENSG00000271052	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12631095	0.86[JPT][hapmap]
rs12632351	1.00[CHD][hapmap]
rs12632514	0.85[CHD][hapmap]
rs12632537	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12632686	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12634319	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs12634781	0.86[JPT][hapmap]
rs16832203	0.88[EUR][1000 genomes]
rs28713364	0.82[EUR][1000 genomes]
rs462514	0.88[JPT][hapmap]
rs56230831	0.84[ASN][1000 genomes]
rs57278490	0.95[EUR][1000 genomes]
rs57496534	0.95[EUR][1000 genomes]
rs57803909	0.95[EUR][1000 genomes]
rs57916312	0.86[EUR][1000 genomes]
rs57974280	0.82[EUR][1000 genomes]
rs58350275	0.95[EUR][1000 genomes]
rs58550445	0.86[ASN][1000 genomes]
rs58557417	0.88[EUR][1000 genomes]
rs58562874	0.95[EUR][1000 genomes]
rs58878734	0.82[EUR][1000 genomes]
rs59541314	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59761692	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59964190	0.95[EUR][1000 genomes]
rs60400555	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60612225	0.95[EUR][1000 genomes]
rs60684226	0.95[EUR][1000 genomes]
rs61217744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441363	1.00[CEU][hapmap]
rs6788738	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs72494864	0.81[ASN][1000 genomes]
rs73878306	0.86[ASN][1000 genomes]
rs73878307	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73878308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73878311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73878313	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73878321	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73878322	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73878324	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73878325	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73878328	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7625217	0.95[EUR][1000 genomes]
rs873183	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs896080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834806	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
3	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv963570	chr3:161076656-161088849	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12634006	C3orf57	cis	multi-tissue	Pritchard

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161059800-161089200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:161081800-161087200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:161082200-161083800	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr3:161082800-161084400	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr3:161083000-161083800	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr3:161083000-161084000	Enhancers	H1 Cell Line	embryonic stem cell
7	chr3:161083000-161084000	Enhancers	H9 Cell Line	embryonic stem cell
8	chr3:161083000-161084400	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr3:161083000-161084800	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr3:161083200-161084400	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr3:161083200-161084600	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr3:161083200-161084800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:161083600-161084400	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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