Variant report

Variant	rs11231151
Chromosome Location	chr11:62351946-62351947
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:62340576..62343284-chr11:62347782..62352195,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254772	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1061093	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11231138	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11231141	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11231144	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11231145	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11231150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11231152	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11231154	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11231155	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11231156	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11231161	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11553576	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12049914	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12223627	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12225213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12226821	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12808829	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17773169	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1801144	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2428548	0.83[EUR][1000 genomes]
rs2428549	0.83[EUR][1000 genomes]
rs2428551	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2509961	0.83[EUR][1000 genomes]
rs2509967	0.83[EUR][1000 genomes]
rs2512562	0.83[EUR][1000 genomes]
rs2512563	0.83[EUR][1000 genomes]
rs2516634	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2849030	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2849031	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34065644	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34894392	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35880596	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3923805	0.83[ASN][1000 genomes]
rs58720921	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60098285	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs61296092	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67308910	0.87[ASN][1000 genomes]
rs7124057	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71490390	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71490392	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71490394	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72927213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7928833	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7930896	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7937146	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7942154	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7942991	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7943191	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1441 gene(s)	inside rSNPs	diseases
2	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
3	nsv832180	chr11:62201605-62364828	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
4	nsv532284	chr11:62220043-62630253	Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1401 gene(s)	inside rSNPs	diseases
5	esv3584599	chr11:62262742-62398050	Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
6	nsv832182	chr11:62295575-62462848	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
7	nsv825939	chr11:62326083-62410577	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Active TSS 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 miRNA target site	122 gene(s)	inside rSNPs	diseases
8	nsv497903	chr11:62330308-62608042	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	489 gene(s)	inside rSNPs	diseases
9	nsv555174	chr11:62334096-62496519	Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	243 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11231151	EEF1G///LOC729998	N/A	lymphoblastoid	RTeQTL
rs11231151	MTA2	cis	Esophagus Mucosa	GTEx
rs11231151	EML3	cis	Whole Blood	GTEx
rs11231151	ROM1	cis	Thyroid	GTEx
rs11231151	EML3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62342400-62352600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:62342400-62358200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:62342600-62355000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr11:62342800-62355000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr11:62343000-62352600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr11:62343000-62357000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:62343000-62358200	Weak transcription	Fetal Heart	heart
8	chr11:62343000-62358200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr11:62343200-62356800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr11:62343200-62356800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr11:62343200-62356800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr11:62343400-62355000	Weak transcription	NHDF-Ad	bronchial
13	chr11:62343400-62355400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr11:62343400-62355800	Strong transcription	Brain Germinal Matrix	brain
15	chr11:62343400-62356200	Strong transcription	Primary T cells from cord blood	blood
16	chr11:62343400-62356600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr11:62343400-62356600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:62343400-62356600	Strong transcription	Fetal Thymus	thymus
19	chr11:62343400-62356800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr11:62343600-62356200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr11:62343600-62356600	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr11:62343800-62356800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr11:62344000-62356200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr11:62344200-62356200	Strong transcription	Duodenum Mucosa	Duodenum
25	chr11:62344400-62355000	Weak transcription	HSMMtube	muscle
26	chr11:62344800-62356200	Strong transcription	Fetal Lung	lung
27	chr11:62344800-62356800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr11:62344800-62356800	Strong transcription	Fetal Muscle Leg	muscle
29	chr11:62344800-62356800	Strong transcription	Fetal Stomach	stomach
30	chr11:62344800-62358200	Weak transcription	Right Atrium	heart
31	chr11:62345000-62356800	Strong transcription	Fetal Intestine Large	intestine
32	chr11:62345200-62352800	Weak transcription	Stomach Mucosa	stomach
33	chr11:62345200-62355000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr11:62345200-62355000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr11:62345200-62356800	Strong transcription	Fetal Intestine Small	intestine
36	chr11:62346200-62356600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr11:62346400-62354000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr11:62346400-62354800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr11:62346400-62356800	Strong transcription	Fetal Muscle Trunk	muscle
40	chr11:62346600-62356800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr11:62346600-62358400	Weak transcription	Small Intestine	intestine
42	chr11:62347000-62357600	Weak transcription	Fetal Brain Male	brain
43	chr11:62347200-62355000	Weak transcription	HUVEC	blood vessel
44	chr11:62347800-62355800	Strong transcription	Primary B cells from cord blood	blood
45	chr11:62347800-62356200	Strong transcription	Fetal Brain Female	brain
46	chr11:62348200-62352000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr11:62348200-62356600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:62348200-62356600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr11:62348200-62356600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr11:62348200-62356800	Strong transcription	Stomach Smooth Muscle	stomach

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