Variant report

Variant	rs4794488
Chromosome Location	chr17:46243513-46243514
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:46240659..46244208-chr17:46251439..46255142,4	MCF-7	breast:
2	chr17:46242593..46245429-chr17:46673241..46675379,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108511	Chromatin interaction
ENSG00000233101	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1039840	1.00[CHB][hapmap]
rs10853093	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs11079817	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs11651669	1.00[CHB][hapmap]
rs11655781	1.00[CHB][hapmap]
rs11656941	1.00[CHB][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1349676	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs16954700	1.00[CHB][hapmap]
rs16954904	1.00[CHB][hapmap]
rs16954931	1.00[CHB][hapmap]
rs16955493	1.00[CHB][hapmap]
rs188268	0.81[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1910574	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs208006	0.83[EUR][1000 genomes]
rs208007	0.81[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs208013	0.81[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs208017	0.81[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs208018	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs2123342	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs2325886	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs2924255	0.81[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs2924256	0.81[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs2924258	0.81[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs2938471	1.00[JPT][hapmap]
rs2938480	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs2938482	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs3792693	0.81[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs3792695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4793822	0.90[ASN][1000 genomes]
rs4794427	0.81[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs4794561	1.00[CHB][hapmap]
rs5016303	0.81[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs595874	0.81[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6504100	0.81[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs6504101	0.81[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs6504113	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs7207270	0.81[EUR][1000 genomes]
rs7208796	0.81[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7210959	1.00[CHB][hapmap]
rs7215230	1.00[CHB][hapmap]
rs7217741	1.00[CHB][hapmap]
rs7218167	1.00[CHB][hapmap]
rs7225140	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs8066529	0.81[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs8067485	1.00[CHB][hapmap]
rs8071262	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs8077814	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs8182234	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs9303543	1.00[CHB][hapmap]
rs9303544	1.00[CHB][hapmap]
rs9899753	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9904487	1.00[CHB][hapmap]
rs9911479	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv908576	chr17:46147807-46260366	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4794488	AARSD1	cis	parietal	SCAN
rs4794488	BECN1	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46216400-46251400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr17:46220800-46249000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr17:46230600-46245000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr17:46231000-46243800	Weak transcription	Primary B cells from cord blood	blood
5	chr17:46236000-46250200	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr17:46236200-46244200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr17:46236800-46244200	Strong transcription	Primary T cells from cord blood	blood
8	chr17:46238200-46250800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr17:46238600-46246600	Weak transcription	Thymus	Thymus
10	chr17:46239200-46246400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr17:46239200-46253800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr17:46240000-46246600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr17:46240000-46250400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr17:46240200-46244600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr17:46240200-46246400	Weak transcription	Fetal Thymus	thymus
16	chr17:46240200-46246800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr17:46241000-46245000	Enhancers	GM12878-XiMat	blood
18	chr17:46241000-46250200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr17:46241000-46253200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr17:46241200-46244800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr17:46241200-46244800	Weak transcription	Fetal Intestine Small	intestine
22	chr17:46241200-46246000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr17:46241200-46247400	Weak transcription	Stomach Mucosa	stomach
24	chr17:46241800-46244600	Weak transcription	Liver	Liver
25	chr17:46242600-46244000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr17:46242600-46245200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr17:46242800-46244000	Enhancers	Brain Germinal Matrix	brain
28	chr17:46243200-46243600	Enhancers	HUES48 Cell Line	embryonic stem cell

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