Variant report

Variant	rs3826397
Chromosome Location	chr17:46509447-46509448
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46505182..46508070-chr17:46508849..46511744,2	K562	blood:
2	chr17:46505182..46508631-chr17:46508849..46512538,4	K562	blood:
3	chr17:46432035..46433984-chr17:46508339..46510187,2	K562	blood:

Variant related genes	Relation type
ENSG00000141293	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1553750	0.82[LWK][hapmap];0.94[YRI][hapmap]
rs1912155	0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs2175155	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2938470	0.94[YRI][hapmap]
rs4053432	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4239201	0.94[YRI][hapmap]
rs4267363	0.81[AFR][1000 genomes]
rs4606751	0.94[YRI][hapmap]
rs4794712	0.80[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6504160	0.94[YRI][hapmap]
rs6504210	0.94[YRI][hapmap]
rs6504251	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6504256	0.81[AFR][1000 genomes]
rs7211099	0.94[YRI][hapmap]
rs7211780	0.83[LWK][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs8072002	0.94[YRI][hapmap]
rs9898383	0.94[YRI][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	nsv833469	chr17:46491849-46709406	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
2	esv2761960	chr17:46504489-46529846	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	esv3420538	chr17:46504944-46861553	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	369 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3826397	HOXB13	cis	cerebellum	SCAN
rs3826397	RPRML	cis	parietal	SCAN
rs3826397	SKAP1	cis	lymphoblastoid	seeQTL
rs3826397	ABI3	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46506000-46510200	Weak transcription	K562	blood
2	chr17:46508000-46509600	Enhancers	Primary T cells fromperipheralblood	blood
3	chr17:46508000-46509800	Enhancers	Fetal Thymus	thymus
4	chr17:46508000-46511800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr17:46508000-46517000	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr17:46508000-46517800	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr17:46508200-46510600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr17:46508200-46517000	Weak transcription	Pancreas	Pancrea
9	chr17:46508200-46517200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr17:46508200-46517800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr17:46508400-46512600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr17:46508400-46513800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr17:46508400-46513800	Weak transcription	GM12878-XiMat	blood
14	chr17:46508600-46510600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr17:46508800-46510800	Enhancers	Primary T cells from cord blood	blood
16	chr17:46509000-46511600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr17:46509200-46509600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr17:46509200-46509800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr17:46509200-46510200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr17:46509200-46513800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr17:46509400-46509600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
22	chr17:46509400-46512600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr17:46509400-46513600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links