Variant report

Variant	rs652615
Chromosome Location	chr11:85485450-85485451
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85471983..85474269-chr11:85484169..85487158,2	MCF-7	breast:
2	chr11:85484461..85487220-chr11:85491729..85494428,2	MCF-7	breast:
3	chr11:85484288..85486316-chr11:85486416..85488624,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10898406	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10898410	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10898413	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10898414	0.82[ASN][1000 genomes]
rs10898415	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11604141	0.82[CEU][hapmap]
rs11606656	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs12362853	0.93[ASN][1000 genomes]
rs1445497	0.82[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1445513	0.87[CEU][hapmap]
rs1481700	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1893163	0.88[ASW][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.81[MKK][hapmap];0.87[ASN][1000 genomes]
rs2008890	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2044391	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2044392	0.86[ASN][1000 genomes]
rs2374683	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs290173	0.89[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs290190	0.81[CHB][hapmap]
rs290195	0.81[CHB][hapmap];0.85[YRI][hapmap]
rs290200	0.89[GIH][hapmap]
rs290202	0.81[CHB][hapmap];0.87[GIH][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap]
rs370385	0.81[JPT][hapmap]
rs478089	0.81[ASN][1000 genomes]
rs485485	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs491867	0.86[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs493078	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944538	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs496187	0.90[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs520500	0.80[ASN][1000 genomes]
rs540063	0.86[CHB][hapmap];0.84[GIH][hapmap]
rs550404	0.87[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap]
rs556669	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs556918	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs575013	0.82[ASW][hapmap];0.84[YRI][hapmap]
rs580459	0.87[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs589327	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs597480	0.83[ASW][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.92[YRI][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs623120	0.81[ASN][1000 genomes]
rs630613	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs631410	0.90[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs641393	0.88[ASW][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs644972	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs647912	0.90[CHB][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs667275	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678723	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs679204	0.90[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs680498	0.90[CHB][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap]
rs683105	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689093	0.82[ASN][1000 genomes]
rs7103790	0.88[ASW][hapmap];0.91[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.85[YRI][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7123846	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051155	chr11:85006564-85721261	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv541110	chr11:85006564-85721261	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv2758279	chr11:85180480-85603988	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv2759845	chr11:85180480-85603988	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv832222	chr11:85405712-85603981	Enhancers Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv898050	chr11:85406915-85499290	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv555639	chr11:85436352-85495269	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1047147	chr11:85459235-85594800	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv541114	chr11:85459235-85594800	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	esv2762927	chr11:85468051-85559618	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv1052737	chr11:85477084-85554914	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv541115	chr11:85477084-85554914	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs652615	GRM5	cis	parietal	SCAN
rs652615	SYTL2	cis	cerebellum	SCAN
rs652615	SYTL2	cis	Muscle Skeletal	GTEx
rs652615	SYTL2	cis	Nerve Tibial	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85474000-85487400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:85475600-85488200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:85478200-85486200	Weak transcription	Small Intestine	intestine
4	chr11:85478600-85486200	Weak transcription	Colonic Mucosa	Colon
5	chr11:85480200-85491800	Weak transcription	Gastric	stomach
6	chr11:85482400-85486000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr11:85483200-85485600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr11:85483200-85492800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:85483400-85486000	Enhancers	NHDF-Ad	bronchial
10	chr11:85483400-85486200	Enhancers	Fetal Kidney	kidney
11	chr11:85483400-85486200	Enhancers	NHLF	lung
12	chr11:85483600-85485800	Enhancers	Fetal Lung	lung
13	chr11:85483600-85486000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr11:85483800-85486400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr11:85484200-85486400	Enhancers	Primary T cells from cord blood	blood
16	chr11:85484200-85486800	Enhancers	Fetal Intestine Large	intestine
17	chr11:85484200-85488000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr11:85484200-85488200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr11:85484400-85486400	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr11:85484400-85486400	Enhancers	HSMM	muscle
21	chr11:85484400-85486400	Enhancers	HSMMtube	muscle
22	chr11:85484400-85488000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr11:85484400-85488000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr11:85484400-85488000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr11:85484400-85488200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr11:85484600-85486400	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr11:85484600-85487200	Enhancers	Stomach Mucosa	stomach
28	chr11:85484600-85488000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr11:85484600-85488000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr11:85484600-85488200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr11:85484600-85488200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr11:85484600-85488200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr11:85484600-85490800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr11:85485000-85485600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr11:85485000-85486600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr11:85485200-85486000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr11:85485200-85486000	Enhancers	NH-A	brain
38	chr11:85485200-85486400	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr11:85485200-85486400	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr11:85485200-85486400	Enhancers	Duodenum Mucosa	Duodenum
41	chr11:85485200-85486600	Enhancers	Fetal Intestine Small	intestine
42	chr11:85485200-85487400	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr11:85485400-85485600	Enhancers	Aorta	Aorta
44	chr11:85485400-85485600	Enhancers	Ovary	ovary
45	chr11:85485400-85485600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr11:85485400-85486000	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr11:85485400-85486000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr11:85485400-85486000	Enhancers	Fetal Muscle Leg	muscle
49	chr11:85485400-85486200	Enhancers	Primary T cells fromperipheralblood	blood
50	chr11:85485400-85486200	Enhancers	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links