Variant report

Variant	rs1534576
Chromosome Location	chr11:47419663-47419664
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47413050..47415602-chr11:47418934..47421513,3	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10437655	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10742802	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10742814	0.84[GIH][hapmap]
rs10769263	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10769264	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10838702	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10838705	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10838709	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10838726	0.87[CHB][hapmap]
rs11039221	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039225	0.84[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039244	0.84[CEU][hapmap];0.94[CHB][hapmap]
rs11606287	0.92[CEU][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs12292911	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1377416	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2242081	0.84[GIH][hapmap]
rs2278890	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2293576	0.84[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];0.87[ASN][1000 genomes]
rs2293579	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35032070	0.87[EUR][1000 genomes]
rs3740699	0.84[GIH][hapmap]
rs3758675	0.83[EUR][1000 genomes]
rs3824869	0.88[CEU][hapmap]
rs4434960	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61897431	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6485758	0.94[CHB][hapmap]
rs7103648	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7104036	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7933019	0.87[CHB][hapmap]
rs7947450	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs874896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs896817	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv825871	chr11:47376020-47457537	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv554210	chr11:47380593-47449544	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
8	nsv541034	chr11:47404083-47440081	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
9	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1534576	C1QTNF4	cis	multi-tissue	Pritchard
rs1534576	MYBPC3	cis	multi-tissue	Pritchard
rs1534576	MTCH2	cis	cerebellum	SCAN
rs1534576	SPI1	cis	multi-tissue	Pritchard
rs1534576	C1QTNF4	cis	lymphoblastoid	seeQTL
rs1534576	MADD	cis	parietal	SCAN
rs1534576		cis	Lymphoblastoid	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47399400-47421400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr11:47399800-47421200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr11:47400000-47421200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr11:47410200-47421200	Weak transcription	Fetal Intestine Small	intestine
5	chr11:47414600-47421200	Weak transcription	Stomach Mucosa	stomach
6	chr11:47415200-47421200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:47415400-47421200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr11:47415400-47421400	Weak transcription	Right Atrium	heart
9	chr11:47415600-47419800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr11:47415600-47421400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr11:47416200-47419800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr11:47416200-47420000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr11:47416200-47421400	Weak transcription	Liver	Liver
14	chr11:47416400-47422000	Weak transcription	HSMM	muscle
15	chr11:47416600-47419800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr11:47416600-47421200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:47416600-47421400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr11:47416600-47421400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:47416800-47419800	Weak transcription	Esophagus	oesophagus
20	chr11:47416800-47421200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr11:47416800-47421200	Weak transcription	Osteobl	bone
22	chr11:47416800-47421400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr11:47416800-47421400	Weak transcription	NH-A	brain
24	chr11:47416800-47421800	Weak transcription	NHLF	lung
25	chr11:47417000-47421200	Weak transcription	Fetal Stomach	stomach
26	chr11:47417000-47421400	Weak transcription	Left Ventricle	heart
27	chr11:47417200-47421000	Enhancers	Primary B cells from peripheral blood	blood
28	chr11:47417200-47421000	Weak transcription	Thymus	Thymus
29	chr11:47417200-47421200	Weak transcription	Right Ventricle	heart
30	chr11:47417200-47421200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr11:47417400-47421200	Enhancers	Primary hematopoietic stem cells	blood
32	chr11:47417400-47421200	Weak transcription	Colonic Mucosa	Colon
33	chr11:47417400-47421200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr11:47417400-47421400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr11:47417600-47420400	Weak transcription	Fetal Muscle Leg	muscle
36	chr11:47417600-47421200	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr11:47417600-47421200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr11:47417600-47421200	Weak transcription	Brain Anterior Caudate	brain
39	chr11:47417600-47421200	Weak transcription	Brain Substantia Nigra	brain
40	chr11:47417600-47421200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr11:47417600-47421200	Weak transcription	HUVEC	blood vessel
42	chr11:47417800-47420200	Weak transcription	Placenta	Placenta
43	chr11:47417800-47420200	Weak transcription	GM12878-XiMat	blood
44	chr11:47417800-47421000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr11:47417800-47421000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr11:47417800-47421000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr11:47417800-47421000	Weak transcription	Spleen	Spleen
48	chr11:47417800-47421200	Weak transcription	Primary T cells from cord blood	blood
49	chr11:47417800-47421200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr11:47417800-47421200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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