Variant report

Variant	rs12822967
Chromosome Location	chr12:66662630-66662631
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10748037	1.00[CEU][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes]
rs10784519	1.00[CEU][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs10784520	0.96[EUR][1000 genomes]
rs10878396	1.00[CEU][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs10878397	0.96[EUR][1000 genomes]
rs10878402	0.81[CEU][hapmap]
rs10878403	0.81[CEU][hapmap]
rs11176115	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11176117	0.89[EUR][1000 genomes]
rs11176120	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11176125	0.81[CEU][hapmap]
rs1168324	0.94[EUR][1000 genomes]
rs12146776	0.87[EUR][1000 genomes]
rs12371662	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12423377	1.00[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs12818303	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1603244	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1816562	1.00[CEU][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes]
rs2047236	0.86[EUR][1000 genomes]
rs2047237	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2088169	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2118137	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs289065	0.97[EUR][1000 genomes]
rs6421217	0.83[CEU][hapmap]
rs6581669	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7137005	0.97[EUR][1000 genomes]
rs7137378	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7138034	0.87[EUR][1000 genomes]
rs724739	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs724742	0.92[CEU][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes]
rs7308068	0.83[CEU][hapmap]
rs7315361	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7959802	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7972934	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9971666	0.90[EUR][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12822967	HELB	cis	parietal	SCAN
rs12822967	HELB	cis	cerebellum	SCAN

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	chr12:66661400-66663000	Enhancers	NHEK	skin
11	chr12:66661600-66663200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:66661600-66663200	Weak transcription	Brain Hippocampus Middle	brain
13	chr12:66661600-66665600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:66662000-66662800	Enhancers	Primary hematopoietic stem cells	blood
15	chr12:66662000-66663400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:66662000-66663400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:66662000-66663600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr12:66662000-66663800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr12:66662000-66663800	Enhancers	Fetal Thymus	thymus
20	chr12:66662000-66664000	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr12:66662000-66664600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:66662000-66664600	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr12:66662200-66662800	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr12:66662200-66662800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:66662200-66663400	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr12:66662200-66663600	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr12:66662400-66662800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:66662400-66664800	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr12:66662600-66662800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:66662600-66663000	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr12:66662600-66663200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
32	chr12:66662600-66664600	Enhancers	Primary T killer memory cells from peripheral blood	blood

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