Variant report

Variant	rs974349
Chromosome Location	chr12:66690949-66690950
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	chr12:66683126..66684829-chr12:66689529..66692193,2	MCF-7	breast:
2	chr12:66689727..66691843-chr12:66693276..66695026,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1009211	0.99[EUR][1000 genomes]
rs10748037	0.81[CEU][hapmap]
rs10748038	0.85[CHB][hapmap]
rs10784519	0.81[CEU][hapmap]
rs10784523	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10878396	0.81[CEU][hapmap]
rs10878401	0.99[EUR][1000 genomes]
rs10878402	1.00[CEU][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs10878403	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176125	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs11176126	0.99[EUR][1000 genomes]
rs11176132	0.98[EUR][1000 genomes]
rs11610967	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs12146707	0.95[EUR][1000 genomes]
rs12146757	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12146776	0.86[EUR][1000 genomes]
rs12423377	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs12822052	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1370125	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1816562	0.81[CEU][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs1898305	0.82[CHB][hapmap]
rs1921013	0.92[CEU][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs2028095	0.96[EUR][1000 genomes]
rs2118138	0.96[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs2118139	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2118140	0.96[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs2904497	0.97[EUR][1000 genomes]
rs3741604	0.92[CEU][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes]
rs3741605	0.96[CEU][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4382951	0.80[AFR][1000 genomes]
rs4430553	0.81[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs6421217	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs6581672	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7131920	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7132724	0.86[CHB][hapmap]
rs7133479	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7306114	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7308068	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7315361	0.80[CEU][hapmap]
rs7316880	0.86[CHB][hapmap]
rs7959802	0.81[CEU][hapmap]
rs7964860	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs7968129	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7969887	0.86[CHB][hapmap]
rs7972934	0.83[CEU][hapmap]
rs7978354	0.86[CHB][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	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv899216	chr12:66563835-66716844	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs974349	C12orf56	cis	cerebellum	SCAN
rs974349	HELB	cis	Nerve Tibial	GTEx
rs974349	HELB	cis	Muscle Skeletal	GTEx
rs974349	HELB	cis	cerebellum	SCAN
rs974349	HELB	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66685000-66691400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:66688000-66695600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr12:66689000-66691600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr12:66689400-66691600	Enhancers	Primary T cells from cord blood	blood
5	chr12:66689400-66691600	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr12:66689600-66691600	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr12:66689800-66691600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:66690000-66691400	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr12:66690000-66691600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr12:66690400-66691400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr12:66690600-66691600	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr12:66690800-66691200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:66690800-66691400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:66690800-66691400	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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