Variant report

Variant	rs12423377
Chromosome Location	chr12:66672458-66672459
allele	A/C
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	RAD21	chr12:66672443-66673495	SK-N-SH	brain:	n/a	chr12:66673101-66673120

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:66561793..66564374-chr12:66672435..66674661,2	MCF-7	breast:

Variant related genes	Relation type
PDCL3P7	TF binding region
ENSG00000155957	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1009211	0.80[EUR][1000 genomes]
rs10748037	1.00[CEU][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs10784519	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784520	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878396	1.00[CEU][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs10878397	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878401	0.80[EUR][1000 genomes]
rs10878402	0.81[CEU][hapmap];0.84[CHB][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs10878403	0.81[CEU][hapmap]
rs11176115	0.89[EUR][1000 genomes]
rs11176117	0.87[EUR][1000 genomes]
rs11176120	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11176125	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs11176126	0.80[EUR][1000 genomes]
rs11176132	0.80[EUR][1000 genomes]
rs11610967	0.88[CHB][hapmap]
rs1168324	0.98[EUR][1000 genomes]
rs12146776	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12371662	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12818303	0.86[EUR][1000 genomes]
rs12819421	0.90[CHB][hapmap]
rs12822967	0.96[EUR][1000 genomes]
rs1603244	0.85[EUR][1000 genomes]
rs1816562	1.00[CEU][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs2047236	0.84[EUR][1000 genomes]
rs2047237	0.87[EUR][1000 genomes]
rs2088169	0.86[EUR][1000 genomes]
rs2118137	0.86[EUR][1000 genomes]
rs289065	0.95[EUR][1000 genomes]
rs2904497	0.81[EUR][1000 genomes]
rs3741604	0.84[CHB][hapmap]
rs6421217	0.83[CEU][hapmap];0.88[CHB][hapmap]
rs6581669	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7137005	0.96[EUR][1000 genomes]
rs7137378	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7138034	0.85[EUR][1000 genomes]
rs724739	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs724742	0.92[CEU][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs7308068	0.83[CEU][hapmap]
rs7315361	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7959802	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7972934	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9971666	0.88[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	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
4	nsv976638	chr12:66669568-66672732	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12423377	HELB	Cis_1M	lymphoblastoid	RTeQTL
rs12423377	HELB	cis	cerebellum	SCAN
rs12423377	HELB	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66664400-66673000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:66664600-66672800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr12:66664600-66672800	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr12:66664600-66673000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr12:66667600-66672800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:66669600-66673000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr12:66670000-66672600	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr12:66670000-66672800	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr12:66670200-66672800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:66670200-66673000	Weak transcription	Primary T cells from cord blood	blood
11	chr12:66670400-66672600	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr12:66672200-66672600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:66672200-66672800	Enhancers	HMEC	breast
14	chr12:66672400-66673000	Enhancers	HUVEC	blood vessel

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