Variant report

Variant	rs520629
Chromosome Location	chr11:85476019-85476020
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85473245..85476644-chr11:85486524..85489414,3	MCF-7	breast:
2	chr11:85446637..85448828-chr11:85475522..85477132,2	MCF-7	breast:
3	chr11:85467154..85470617-chr11:85475521..85479674,4	MCF-7	breast:
4	chr11:85475609..85477419-chr11:85479383..85481786,2	K562	blood:
5	chr11:85470232..85472552-chr11:85473605..85477376,4	K562	blood:

Variant related genes	Relation type
ENSG00000137501	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11234410	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1151152	0.95[ASN][1000 genomes]
rs11604141	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11604178	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11606818	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs12792050	0.95[ASN][1000 genomes]
rs1445513	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17817179	0.84[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.92[TSI][hapmap];0.89[ASN][1000 genomes]
rs188311	0.96[CEU][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs2467059	0.81[JPT][hapmap]
rs290175	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs290177	0.81[JPT][hapmap]
rs290186	0.81[JPT][hapmap]
rs290190	0.83[CEU][hapmap]
rs290194	0.91[CEU][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs290195	0.83[CEU][hapmap]
rs290196	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs290199	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs290200	0.92[CEU][hapmap]
rs290202	0.84[CEU][hapmap]
rs3862785	0.84[CHB][hapmap]
rs491867	0.87[CEU][hapmap]
rs493673	0.85[AMR][1000 genomes]
rs4944539	0.89[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap]
rs496187	0.87[CEU][hapmap]
rs497158	0.93[ASN][1000 genomes]
rs510948	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs521764	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs537266	0.95[CEU][hapmap];0.80[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs537604	0.87[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs540063	0.91[CEU][hapmap]
rs543995	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs550404	0.83[CEU][hapmap]
rs556669	0.83[CEU][hapmap]
rs558377	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs565494	0.96[ASN][1000 genomes]
rs56579	0.81[JPT][hapmap]
rs573766	0.87[CEU][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes]
rs578324	0.95[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs580459	0.83[CEU][hapmap]
rs583122	0.95[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs589327	0.83[CEU][hapmap]
rs592380	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs592712	0.91[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.89[ASN][1000 genomes]
rs609012	0.91[CEU][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.87[ASN][1000 genomes]
rs613973	0.91[CEU][hapmap];0.82[ASN][1000 genomes]
rs61907272	0.90[ASN][1000 genomes]
rs631104	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs631410	0.87[CEU][hapmap]
rs639688	0.87[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs644558	0.95[ASN][1000 genomes]
rs644972	0.87[CEU][hapmap]
rs647912	0.87[CEU][hapmap]
rs650036	0.91[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs650970	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs653559	0.96[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs666176	0.89[ASN][1000 genomes]
rs667080	0.93[ASN][1000 genomes]
rs679204	0.83[CEU][hapmap]
rs680498	0.87[CEU][hapmap]
rs681044	0.91[CEU][hapmap];0.84[CHB][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs683903	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs688741	0.91[CEU][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1054027	chr11:85429074-85477283	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs520629	SYTL2	cis	cerebellum	SCAN
rs520629	ME3	cis	cerebellum	SCAN
rs520629	GRM5	cis	parietal	SCAN
rs520629	RAB38	cis	cerebellum	SCAN
rs520629	SYTL2	cis	lymphoblastoid	seeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85430400-85480400	Weak transcription	Aorta	Aorta
2	chr11:85448000-85480600	Weak transcription	Fetal Stomach	stomach
3	chr11:85449200-85478400	Weak transcription	Right Ventricle	heart
4	chr11:85460600-85483800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:85463200-85478800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr11:85467600-85477600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr11:85469400-85485400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr11:85469800-85477000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr11:85469800-85477800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr11:85471200-85477400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr11:85471600-85476400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr11:85471600-85477600	Weak transcription	NHLF	lung
13	chr11:85471800-85482600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr11:85471800-85483200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr11:85472000-85477000	Weak transcription	Small Intestine	intestine
16	chr11:85472000-85480600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:85472000-85481200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr11:85472000-85485400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr11:85472200-85477800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr11:85472200-85478800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr11:85472600-85484600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr11:85473800-85477600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr11:85473800-85477600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr11:85473800-85477800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr11:85474000-85487400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr11:85474200-85477000	Weak transcription	NHDF-Ad	bronchial
27	chr11:85474600-85477800	Enhancers	Fetal Kidney	kidney
28	chr11:85475200-85481000	Weak transcription	Primary T cells from cord blood	blood
29	chr11:85475600-85488200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr11:85475800-85478200	Weak transcription	Stomach Mucosa	stomach
31	chr11:85476000-85477200	Weak transcription	HSMMtube	muscle
32	chr11:85476000-85482400	Weak transcription	HSMM	muscle

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