Variant report

Variant	rs667275
Chromosome Location	chr11:85484416-85484417
allele	C/T
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	chr11:85484288..85486316-chr11:85486416..85488624,2	MCF-7	breast:
3	chr11:85483031..85484829-chr11:85489354..85491386,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10898406	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10898410	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10898413	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10898414	0.82[ASN][1000 genomes]
rs10898415	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11604141	0.82[CEU][hapmap]
rs11606656	0.82[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs12362853	0.93[ASN][1000 genomes]
rs1445497	0.95[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1445513	0.87[CEU][hapmap]
rs1481700	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1893163	0.95[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2008890	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2044391	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2044392	0.86[ASN][1000 genomes]
rs2374683	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs290173	0.86[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs290190	0.81[CHB][hapmap]
rs290195	0.81[CHB][hapmap]
rs290200	0.86[GIH][hapmap]
rs290202	0.81[CHB][hapmap];0.85[GIH][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap]
rs370385	0.81[JPT][hapmap]
rs478089	0.81[ASN][1000 genomes]
rs485485	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs491867	0.86[CHB][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap]
rs493078	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944538	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs496187	0.90[CHB][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap]
rs520500	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs540063	0.86[CHB][hapmap];0.82[GIH][hapmap]
rs550404	0.87[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs556669	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs556918	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs580459	0.87[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap]
rs589327	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs597480	0.87[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][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];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs631410	0.90[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs641393	0.87[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs644972	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs647912	0.84[ASW][hapmap];0.90[CHB][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs652615	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678723	0.81[ASN][1000 genomes]
rs679204	0.90[CHB][hapmap];0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs680498	0.90[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs683105	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689093	0.82[ASN][1000 genomes]
rs7103790	0.91[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.88[ASN][1000 genomes]
rs7123846	0.86[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
rs667275	SYTL2	cis	cerebellum	SCAN
rs667275	SYTL2	cis	Muscle Skeletal	GTEx
rs667275	SYTL2	cis	Nerve Tibial	GTEx
rs667275	GRM5	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85469400-85485400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr11:85472000-85485400	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr11:85472600-85484600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr11:85474000-85487400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:85475600-85488200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr11:85478200-85486200	Weak transcription	Small Intestine	intestine
7	chr11:85478600-85486200	Weak transcription	Colonic Mucosa	Colon
8	chr11:85479200-85485400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr11:85479800-85485200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr11:85480200-85491800	Weak transcription	Gastric	stomach
11	chr11:85482000-85485400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr11:85482400-85486000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr11:85482600-85484600	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr11:85482600-85484600	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr11:85482600-85485000	Enhancers	Ovary	ovary
16	chr11:85482800-85485200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr11:85483000-85484600	Enhancers	Fetal Stomach	stomach
18	chr11:85483200-85484600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr11:85483200-85485600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr11:85483200-85492800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr11:85483400-85484600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr11:85483400-85484600	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr11:85483400-85484600	Enhancers	Muscle Satellite Cultured Cells	--
24	chr11:85483400-85486000	Enhancers	NHDF-Ad	bronchial
25	chr11:85483400-85486200	Enhancers	Fetal Kidney	kidney
26	chr11:85483400-85486200	Enhancers	NHLF	lung
27	chr11:85483600-85484600	Enhancers	H1 Cell Line	embryonic stem cell
28	chr11:85483600-85484800	Enhancers	NH-A	brain
29	chr11:85483600-85485800	Enhancers	Fetal Lung	lung
30	chr11:85483600-85486000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr11:85483800-85484600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr11:85483800-85486400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr11:85484000-85484600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr11:85484000-85484600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
35	chr11:85484000-85485000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr11:85484000-85485200	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr11:85484200-85484600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr11:85484200-85484600	Weak transcription	Stomach Mucosa	stomach
39	chr11:85484200-85484800	Enhancers	Fetal Intestine Small	intestine
40	chr11:85484200-85486400	Enhancers	Primary T cells from cord blood	blood
41	chr11:85484200-85486800	Enhancers	Fetal Intestine Large	intestine
42	chr11:85484200-85488000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr11:85484200-85488200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr11:85484400-85485400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr11:85484400-85485400	Weak transcription	Aorta	Aorta
46	chr11:85484400-85485400	Weak transcription	Fetal Muscle Leg	muscle
47	chr11:85484400-85486400	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr11:85484400-85486400	Enhancers	HSMM	muscle
49	chr11:85484400-85486400	Enhancers	HSMMtube	muscle
50	chr11:85484400-85488000	Weak transcription	H9 Cell Line	embryonic stem cell

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