Variant report

Variant	rs493078
Chromosome Location	chr11:85483310-85483311
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:85483031..85484829-chr11:85489354..85491386,2	MCF-7	breast:

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10898406	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10898410	0.83[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10898413	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10898414	0.82[ASN][1000 genomes]
rs10898415	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11603256	0.84[JPT][hapmap]
rs11606656	0.86[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs12362853	0.93[ASN][1000 genomes]
rs1237203	0.82[JPT][hapmap]
rs1445497	0.86[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1481700	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs188311	0.91[CEU][hapmap]
rs1893163	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2008890	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2044391	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2044392	0.86[ASN][1000 genomes]
rs2196168	0.84[JPT][hapmap]
rs2374683	0.83[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs290173	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs290174	0.84[EUR][1000 genomes]
rs290175	0.91[CEU][hapmap]
rs290185	0.83[JPT][hapmap]
rs290190	0.95[CEU][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs290191	0.85[EUR][1000 genomes]
rs290194	0.87[CEU][hapmap]
rs290195	0.86[CEU][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs290196	0.91[CEU][hapmap]
rs290199	0.86[CEU][hapmap]
rs290200	0.86[CEU][hapmap];0.84[JPT][hapmap]
rs290202	0.95[CEU][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes]
rs370385	0.90[JPT][hapmap]
rs3753050	0.84[JPT][hapmap]
rs3781815	0.83[JPT][hapmap]
rs3862782	0.84[JPT][hapmap]
rs475491	0.88[EUR][1000 genomes]
rs478089	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs485485	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs491867	0.81[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap]
rs4944538	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs496187	0.81[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap]
rs510948	0.91[CEU][hapmap]
rs520500	0.80[ASN][1000 genomes]
rs520629	0.86[CEU][hapmap]
rs537266	0.90[CEU][hapmap]
rs537604	0.91[CEU][hapmap]
rs540063	0.86[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap]
rs550404	0.86[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap]
rs556669	0.87[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap]
rs556918	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs573766	0.82[CEU][hapmap]
rs578324	0.90[CEU][hapmap]
rs580459	0.86[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap]
rs583122	0.82[CEU][hapmap]
rs589327	0.95[CEU][hapmap];0.85[CHB][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs592712	0.95[CEU][hapmap]
rs594892	0.81[AMR][1000 genomes]
rs597480	0.91[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs609012	0.86[CEU][hapmap]
rs613973	0.87[CEU][hapmap]
rs623120	0.81[ASN][1000 genomes]
rs630613	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs631410	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs639688	0.86[CEU][hapmap]
rs641393	0.91[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs644972	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs647912	0.91[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs650036	0.86[CEU][hapmap]
rs652615	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs653559	0.82[CEU][hapmap]
rs667275	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675513	0.81[EUR][1000 genomes]
rs678723	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs679204	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs680498	0.91[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap]
rs681044	0.87[CEU][hapmap]
rs683105	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs688741	0.86[CEU][hapmap]
rs689093	0.82[ASN][1000 genomes]
rs7103790	0.86[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs7107788	0.84[JPT][hapmap]
rs7123846	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs956202	0.84[JPT][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs493078	SYTL2	cis	Muscle Skeletal	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85460600-85483800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:85469400-85485400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr11:85472000-85485400	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr11:85472600-85484600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr11:85474000-85487400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:85475600-85488200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr11:85478200-85486200	Weak transcription	Small Intestine	intestine
8	chr11:85478600-85483400	Weak transcription	NHLF	lung
9	chr11:85478600-85486200	Weak transcription	Colonic Mucosa	Colon
10	chr11:85478800-85484000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:85479200-85483400	Weak transcription	NHDF-Ad	bronchial
12	chr11:85479200-85484000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr11:85479200-85485400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr11:85479400-85483600	Weak transcription	Stomach Mucosa	stomach
15	chr11:85479400-85483800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr11:85479400-85484000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr11:85479800-85485200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr11:85480000-85484400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr11:85480200-85483400	Weak transcription	Fetal Kidney	kidney
20	chr11:85480200-85491800	Weak transcription	Gastric	stomach
21	chr11:85481200-85484000	Weak transcription	Aorta	Aorta
22	chr11:85481200-85484200	Weak transcription	Primary T cells from cord blood	blood
23	chr11:85481200-85484200	Weak transcription	Fetal Intestine Small	intestine
24	chr11:85481600-85484200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr11:85482000-85483600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr11:85482000-85485400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr11:85482200-85483400	Enhancers	HSMMtube	muscle
28	chr11:85482400-85484000	Enhancers	HSMM	muscle
29	chr11:85482400-85486000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:85482600-85484400	Enhancers	Fetal Muscle Leg	muscle
31	chr11:85482600-85484600	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr11:85482600-85484600	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr11:85482600-85485000	Enhancers	Ovary	ovary
34	chr11:85482800-85483400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr11:85482800-85483600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr11:85482800-85484000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr11:85482800-85485200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr11:85483000-85483400	Enhancers	Fetal Muscle Trunk	muscle
39	chr11:85483000-85484600	Enhancers	Fetal Stomach	stomach
40	chr11:85483200-85484200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr11:85483200-85484400	Enhancers	Fetal Heart	heart
42	chr11:85483200-85484600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr11:85483200-85485600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr11:85483200-85492800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links