Variant report

Variant	rs537266
Chromosome Location	chr11:85433687-85433688
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr11:85433656-85434833	MCF-7	breast:	n/a	chr11:85434732-85434743 chr11:85433993-85434002 chr11:85433986-85434007 chr11:85433989-85434005

No.	Distal block	Cell Line	Cell type
1	chr11:85432781..85434564-chr11:85442681..85445528,2	MCF-7	breast:
2	chr11:85427809..85429920-chr11:85433567..85435878,3	MCF-7	breast:
3	chr11:85406368..85408240-chr11:85432667..85435313,3	MCF-7	breast:
4	chr11:85414305..85416177-chr11:85432869..85434542,2	MCF-7	breast:
5	chr11:85433132..85435744-chr11:85522806..85525692,2	MCF-7	breast:
6	chr11:85430781..85433694-chr11:85551714..85553918,2	MCF-7	breast:

Variant related genes	Relation type
SYTL2	TF binding region
ENSG00000137501	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10501595	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs11234359	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs11234410	0.86[EUR][1000 genomes]
rs11604141	0.85[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap]
rs1192	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs1214001	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs12419172	0.94[JPT][hapmap]
rs1445513	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs17208492	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs17208519	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs17810659	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs17817179	0.81[CHB][hapmap];0.81[TSI][hapmap]
rs188311	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1892872	0.94[JPT][hapmap]
rs1991923	0.94[JPT][hapmap]
rs2290823	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs2467059	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs290172	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs290173	0.80[CEU][hapmap]
rs290175	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs290177	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs290178	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs290182	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs290186	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs290190	0.87[CEU][hapmap]
rs290194	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs290195	0.83[CEU][hapmap]
rs290196	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs290197	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs290199	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs290200	0.87[CEU][hapmap]
rs290202	0.88[CEU][hapmap]
rs487964	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs489896	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs491867	0.87[CEU][hapmap];0.84[MEX][hapmap];0.92[YRI][hapmap]
rs493673	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4943925	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs4944529	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs4944531	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs496187	0.87[CEU][hapmap];0.84[MEX][hapmap];0.92[YRI][hapmap]
rs510948	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs520629	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]
rs521764	0.85[EUR][1000 genomes]
rs537604	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs540063	0.91[CEU][hapmap]
rs550404	0.92[CEU][hapmap]
rs556669	0.92[CEU][hapmap];0.92[YRI][hapmap]
rs558377	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56579	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs573766	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs578324	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs580459	0.92[CEU][hapmap];0.84[MEX][hapmap];0.92[YRI][hapmap]
rs583122	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs589327	0.91[CEU][hapmap]
rs592380	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs592712	0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap]
rs597480	0.88[CEU][hapmap]
rs609012	0.91[CEU][hapmap];0.90[CHB][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap]
rs613973	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs631104	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs631410	0.87[CEU][hapmap]
rs639688	0.95[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap]
rs640620	0.81[ASN][1000 genomes]
rs641393	0.88[CEU][hapmap]
rs644972	0.87[CEU][hapmap]
rs647912	0.87[CEU][hapmap]
rs650036	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs650970	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs653559	0.84[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs679204	0.91[CEU][hapmap]
rs680498	0.96[CEU][hapmap];0.84[MEX][hapmap]
rs681044	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.84[ASN][1000 genomes]
rs688741	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs7119617	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs7943586	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs7948778	0.85[CHB][hapmap]
rs881121	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs947861	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs947863	0.85[CHB][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 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	nsv468768	chr11:85395180-85436352	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv555632	chr11:85395180-85436352	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv1052123	chr11:85425856-85471132	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking 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
10	nsv555633	chr11:85426330-85473883	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription 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
11	nsv1036110	chr11:85429074-85471132	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	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
13	esv3471508	chr11:85429687-85472395	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	esv3471519	chr11:85429687-85472395	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv555634	chr11:85430397-85464922	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv555635	chr11:85430397-85470893	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv555636	chr11:85431886-85465179	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv1042192	chr11:85433687-85464922	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv1039118	chr11:85433687-85468605	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv1039830	chr11:85433687-85470589	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	nsv1047001	chr11:85433687-85470941	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
22	nsv1042942	chr11:85433687-85471132	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs537266	RAB38	cis	cerebellum	SCAN
rs537266	GRM5	cis	parietal	SCAN
rs537266	SYTL2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85397200-85438600	Weak transcription	Colonic Mucosa	Colon
2	chr11:85412000-85436800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr11:85412000-85438000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr11:85417600-85453000	Weak transcription	Gastric	stomach
5	chr11:85418400-85436400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr11:85422600-85448600	Weak transcription	Fetal Intestine Large	intestine
7	chr11:85422800-85448200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr11:85424000-85448600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr11:85430200-85437800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr11:85430400-85434000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr11:85430400-85436000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr11:85430400-85436600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr11:85430400-85437400	Weak transcription	Stomach Mucosa	stomach
14	chr11:85430400-85459000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr11:85430400-85480400	Weak transcription	Aorta	Aorta
16	chr11:85430600-85437200	Weak transcription	Fetal Kidney	kidney
17	chr11:85430600-85447000	Weak transcription	Ovary	ovary
18	chr11:85430800-85434000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:85430800-85434200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr11:85430800-85435200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr11:85430800-85445000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr11:85430800-85447200	Weak transcription	Fetal Stomach	stomach
23	chr11:85430800-85448800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr11:85430800-85459000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr11:85431000-85433800	Weak transcription	HMEC	breast
26	chr11:85431000-85434000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr11:85431000-85434200	Weak transcription	NHEK	skin
28	chr11:85431000-85436400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr11:85431000-85445200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:85431200-85436200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr11:85431200-85436200	Weak transcription	NH-A	brain
32	chr11:85431200-85436600	Weak transcription	Osteobl	bone
33	chr11:85431400-85433800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:85431400-85434000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:85431400-85436400	Weak transcription	A549	lung
36	chr11:85431400-85436600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr11:85431400-85451600	Weak transcription	HSMMtube	muscle
38	chr11:85431600-85436600	Weak transcription	HSMM	muscle
39	chr11:85431800-85435400	Weak transcription	NHLF	lung
40	chr11:85431800-85436600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr11:85431800-85437600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr11:85431800-85466600	Weak transcription	Brain Substantia Nigra	brain
43	chr11:85432000-85434000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr11:85432000-85434200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr11:85432000-85434200	Weak transcription	Primary T cells from cord blood	blood
46	chr11:85432000-85436600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr11:85432000-85436800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr11:85432000-85460800	Weak transcription	Fetal Muscle Leg	muscle
49	chr11:85432200-85448400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr11:85433000-85436000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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