Variant report

Variant	rs17085165
Chromosome Location	chr5:95169503-95169504
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:95167615..95170613-chr5:95172553..95174092,2	MCF-7	breast:
2	chr5:95168597..95170209-chr5:95172089..95173618,2	K562	blood:
3	chr5:95156501..95159437-chr5:95167856..95170336,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173221	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10040697	0.85[CHB][hapmap]
rs12109442	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12109499	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12651950	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12658997	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17085159	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap]
rs17085170	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17085255	1.00[ASW][hapmap]
rs2007	0.82[CHB][hapmap]
rs2546193	0.85[CHB][hapmap]
rs3822751	0.95[CHB][hapmap]
rs4869251	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59044001	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs60682160	0.82[ASN][1000 genomes]
rs6556883	1.00[CHB][hapmap]
rs72656688	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7734301	0.85[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][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	nsv830409	chr5:95006686-95204496	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv882389	chr5:95144952-95173887	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17085165	SLC5A3	trans	brain	seeQTL
rs17085165	DDX6	trans	brain	seeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95159800-95169800	Weak transcription	Fetal Kidney	kidney
2	chr5:95160200-95169800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:95160600-95170000	Weak transcription	Right Atrium	heart
4	chr5:95160600-95170400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:95160800-95169800	Weak transcription	Fetal Heart	heart
6	chr5:95160800-95169800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr5:95161600-95171400	Weak transcription	Small Intestine	intestine
8	chr5:95161800-95169800	Weak transcription	Thymus	Thymus
9	chr5:95161800-95170000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:95162400-95169600	Weak transcription	Hela-S3	cervix
11	chr5:95164200-95171400	Weak transcription	Spleen	Spleen
12	chr5:95164400-95169800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:95164600-95169800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr5:95164800-95169600	Weak transcription	Fetal Intestine Small	intestine
15	chr5:95164800-95170200	Weak transcription	Colonic Mucosa	Colon
16	chr5:95164800-95170400	Weak transcription	Lung	lung
17	chr5:95167400-95169600	Enhancers	Primary T cells from cord blood	blood
18	chr5:95167400-95169600	Enhancers	Dnd41	blood
19	chr5:95167600-95169800	Weak transcription	Colon Smooth Muscle	Colon
20	chr5:95167800-95169800	Weak transcription	Aorta	Aorta
21	chr5:95167800-95170000	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr5:95167800-95170400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:95168000-95169600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr5:95168000-95169800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr5:95168000-95169800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr5:95168000-95169800	Enhancers	GM12878-XiMat	blood
27	chr5:95168000-95170400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr5:95168200-95169800	Enhancers	Primary hematopoietic stem cells	blood
29	chr5:95168200-95169800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr5:95168200-95169800	Enhancers	NHEK	skin
31	chr5:95168200-95170000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr5:95168400-95169600	Enhancers	A549	lung
33	chr5:95168400-95169800	Enhancers	Primary B cells from cord blood	blood
34	chr5:95168400-95169800	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr5:95168400-95170000	Enhancers	Liver	Liver
36	chr5:95168600-95169800	Enhancers	Primary B cells from peripheral blood	blood
37	chr5:95168600-95170000	Enhancers	Primary T cells fromperipheralblood	blood
38	chr5:95168600-95170000	Enhancers	Stomach Mucosa	stomach
39	chr5:95168600-95170200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr5:95168800-95169800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr5:95168800-95169800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr5:95168800-95170000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr5:95168800-95170000	Enhancers	HepG2	liver
44	chr5:95168800-95170200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:95168800-95170400	Enhancers	Placenta	Placenta
46	chr5:95169000-95169600	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr5:95169000-95169800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr5:95169000-95170000	Enhancers	Fetal Intestine Large	intestine
49	chr5:95169000-95170400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:95169200-95169600	Enhancers	Primary T helper cells PMA-I stimulated	--

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