Variant report

Variant	rs7952846
Chromosome Location	chr12:66854354-66854355
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1038923	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10735936	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10748047	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10784538	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10784539	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10784540	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10784541	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10784545	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10784546	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11176191	0.87[ASN][1000 genomes]
rs11176204	0.86[JPT][hapmap]
rs11176205	0.86[JPT][hapmap]
rs11176225	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11560004	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11609808	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12099798	0.90[YRI][hapmap]
rs12229196	0.81[JPT][hapmap]
rs12321126	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1288	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1845296	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3891951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3970925	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4913307	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4913310	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4913496	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4913502	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4913517	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4913518	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6581698	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7132569	0.86[JPT][hapmap]
rs7134378	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7135061	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7306349	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7307274	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7487758	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7960332	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7962122	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9989032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1051713	chr12:66745716-66889411	Strong transcription Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1040682	chr12:66750103-67328053	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv832447	chr12:66785814-66990029	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv469459	chr12:66854354-66950289	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv559206	chr12:66854354-66950289	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7952846	HELB	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66823200-66859000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:66836200-66856600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:66836400-66855200	Weak transcription	Placenta	Placenta
4	chr12:66838800-66858400	Weak transcription	Fetal Brain Female	brain
5	chr12:66843800-66857200	Weak transcription	HMEC	breast
6	chr12:66844000-66861600	Weak transcription	Primary T cells from cord blood	blood
7	chr12:66846800-66860200	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:66849400-66866400	Weak transcription	Pancreas	Pancrea
9	chr12:66849600-66860000	Weak transcription	Esophagus	oesophagus
10	chr12:66851600-66857600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:66853000-66876200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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