Variant report

Variant	rs6581669
Chromosome Location	chr12:66663394-66663395
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	chr12:66562059..66564865-chr12:66662952..66665782,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155957	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10748037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784519	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10784520	0.95[EUR][1000 genomes]
rs10878396	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10878397	0.95[EUR][1000 genomes]
rs11176115	0.89[EUR][1000 genomes]
rs11176117	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11176120	0.96[EUR][1000 genomes]
rs1168324	0.96[EUR][1000 genomes]
rs12146776	0.85[EUR][1000 genomes]
rs12371662	0.95[EUR][1000 genomes]
rs12423377	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12818303	0.88[EUR][1000 genomes]
rs12822967	0.96[EUR][1000 genomes]
rs1603244	0.87[EUR][1000 genomes]
rs1816562	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2047236	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2047237	0.87[EUR][1000 genomes]
rs2088169	0.88[EUR][1000 genomes]
rs2118137	0.88[EUR][1000 genomes]
rs289065	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7137005	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137378	0.97[EUR][1000 genomes]
rs7138034	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs724739	0.94[EUR][1000 genomes]
rs724742	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315361	0.95[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7959802	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972934	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs9971666	0.91[EUR][1000 genomes];0.89[ASN][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	nsv976747	chr12:66663300-66669568	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6581669	HELB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66650800-66663400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:66658200-66663600	Weak transcription	Thymus	Thymus
3	chr12:66660800-66663400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:66660800-66663800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr12:66661000-66664800	Enhancers	Primary T cells from cord blood	blood
6	chr12:66661200-66663600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:66661200-66663600	Enhancers	GM12878-XiMat	blood
8	chr12:66661200-66664600	Enhancers	Primary B cells from cord blood	blood
9	chr12:66661200-66666800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:66661600-66665600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:66662000-66663400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:66662000-66663400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:66662000-66663600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr12:66662000-66663800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr12:66662000-66663800	Enhancers	Fetal Thymus	thymus
16	chr12:66662000-66664000	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr12:66662000-66664600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr12:66662000-66664600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr12:66662200-66663400	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr12:66662200-66663600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr12:66662400-66664800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr12:66662600-66664600	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr12:66662800-66663800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr12:66662800-66663800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr12:66663000-66663400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr12:66663000-66663600	Enhancers	H1 Cell Line	embryonic stem cell
27	chr12:66663200-66663600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:66663200-66663600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:66663200-66663800	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr12:66663200-66663800	Enhancers	Brain Hippocampus Middle	brain
31	chr12:66663200-66664000	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr12:66663200-66665800	Enhancers	Primary monocytes fromperipheralblood	blood

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