Variant report

Variant	rs7940772
Chromosome Location	chr11:86317519-86317520
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:86316921..86319182-chr11:86528850..86531026,2	MCF-7	breast:
2	chr11:86317084..86318773-chr11:86517876..86519532,2	MCF-7	breast:
3	chr11:86315634..86317627-chr11:86511159..86513045,2	MCF-7	breast:
4	chr11:86302794..86305608-chr11:86317191..86320162,2	K562	blood:
5	chr11:86316496..86321662-chr11:86508610..86513631,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150687	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10219173	0.96[ASN][1000 genomes]
rs10219305	0.97[ASN][1000 genomes]
rs10219319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10219378	0.98[ASN][1000 genomes]
rs10400291	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10792860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10792861	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10792862	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10792863	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10792864	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10792866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10898505	0.90[ASN][1000 genomes]
rs10898506	0.83[ASN][1000 genomes]
rs10898507	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10898510	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10898511	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10898512	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[ASN][1000 genomes]
rs10898514	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898515	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10898516	0.85[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11234717	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11535845	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12289252	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12290684	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1540081	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1540082	0.88[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs17211577	0.87[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1894012	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1938924	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1938925	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1938926	0.96[ASN][1000 genomes]
rs1938927	0.94[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1938928	0.87[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1938938	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1945146	0.86[MEX][hapmap];0.81[AMR][1000 genomes]
rs2032356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2051433	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2155035	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2840368	0.87[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4144865	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4944601	0.88[ASN][1000 genomes]
rs4944604	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944610	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944613	0.94[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs722157	0.89[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs722158	0.89[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7940587	1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7940590	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7940781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940788	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs949350	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9634021	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv555665	chr11:86230898-86417553	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1055071	chr11:86301240-86465465	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv898057	chr11:86306401-86335459	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv522823	chr11:86317519-86321576	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7940772	ME3	cis	multi-tissue	Pritchard

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86300200-86318800	Weak transcription	Esophagus	oesophagus
2	chr11:86307000-86317800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:86308800-86321600	Weak transcription	Left Ventricle	heart
4	chr11:86309400-86321600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:86315600-86318800	Weak transcription	Fetal Intestine Small	intestine
6	chr11:86315600-86319000	Weak transcription	Fetal Intestine Large	intestine
7	chr11:86316200-86320200	Enhancers	HUVEC	blood vessel
8	chr11:86316400-86317800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr11:86316400-86320400	Enhancers	Fetal Stomach	stomach
10	chr11:86316800-86319600	Enhancers	Fetal Brain Male	brain
11	chr11:86317000-86318400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:86317000-86318400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:86317000-86319000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:86317000-86319000	Enhancers	Right Ventricle	heart
15	chr11:86317000-86319200	Enhancers	Stomach Smooth Muscle	stomach
16	chr11:86317000-86319200	Enhancers	A549	lung
17	chr11:86317000-86319600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr11:86317000-86319600	Enhancers	Ovary	ovary
19	chr11:86317000-86319800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr11:86317000-86320200	Enhancers	Fetal Heart	heart
21	chr11:86317200-86318400	Enhancers	Fetal Brain Female	brain
22	chr11:86317200-86319000	Enhancers	Colon Smooth Muscle	Colon
23	chr11:86317200-86319200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr11:86317200-86319200	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr11:86317200-86319800	Enhancers	Fetal Muscle Leg	muscle
26	chr11:86317200-86320400	Enhancers	Rectal Smooth Muscle	rectum
27	chr11:86317200-86320400	Enhancers	Hela-S3	cervix
28	chr11:86317400-86317600	Enhancers	Brain Angular Gyrus	brain
29	chr11:86317400-86317600	Enhancers	Right Atrium	heart
30	chr11:86317400-86317800	Enhancers	H1 Cell Line	embryonic stem cell
31	chr11:86317400-86317800	Enhancers	Psoas Muscle	Psoas
32	chr11:86317400-86318400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr11:86317400-86319200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:86317400-86319600	Enhancers	Aorta	Aorta
35	chr11:86317400-86319600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr11:86317400-86320000	Enhancers	Muscle Satellite Cultured Cells	--
37	chr11:86317400-86320000	Enhancers	HSMM	muscle
38	chr11:86317400-86320000	Enhancers	NH-A	brain
39	chr11:86317400-86320000	Enhancers	NHDF-Ad	bronchial
40	chr11:86317400-86320200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr11:86317400-86321600	Weak transcription	Pancreas	Pancrea

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