Variant report

Variant	rs12225213
Chromosome Location	chr11:62350248-62350249
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:62340576..62343284-chr11:62347782..62352195,6	MCF-7	breast:
2	chr11:62348874..62350757-chr11:62606109..62608952,2	K562	blood:
3	chr11:62343656..62346123-chr11:62348412..62350448,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133316	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000254772	Chromatin interaction
ENSG00000255508	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1061093	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11231137	0.80[ASN][1000 genomes]
rs11231138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11231141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11231144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11231145	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11231150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11231151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11231152	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11231154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11231155	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11231156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11231161	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11231176	1.00[JPT][hapmap]
rs11553576	0.96[CEU][hapmap];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];0.96[ASN][1000 genomes]
rs12223627	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12226821	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12808829	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17773169	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1801144	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2428548	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs2428549	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs2428551	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2509961	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs2509967	0.83[EUR][1000 genomes]
rs2509982	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs2512562	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs2512563	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs2516633	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2516634	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2849030	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2849031	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34065644	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34894392	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35156678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs35587183	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs35880596	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3923805	0.89[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];0.83[ASN][1000 genomes]
rs61296092	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67308910	0.93[ASN][1000 genomes]
rs7124057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71490390	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][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];0.96[ASN][1000 genomes]
rs72927213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72927237	0.82[ASN][1000 genomes]
rs7928833	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7930896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];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];0.83[ASN][1000 genomes]
rs7942991	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7943191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12225213	EML3	cis	Whole Blood	GTEx
rs12225213	EML3	cis	Esophagus Mucosa	GTEx
rs12225213	ROM1	cis	Thyroid	GTEx
rs12225213	EEF1G	cis	multi-tissue	Pritchard
rs12225213	MTA2	cis	Esophagus Mucosa	GTEx
rs12225213	EEF1G///LOC729998	N/A	lymphoblastoid	RTeQTL
rs12225213	EML3	cis	multi-tissue	Pritchard

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	chr11:62342800-62351200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:62342800-62355000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr11:62343000-62352600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr11:62343000-62357000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:62343000-62358200	Weak transcription	Fetal Heart	heart
9	chr11:62343000-62358200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr11:62343200-62351400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr11:62343200-62356800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr11:62343200-62356800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr11:62343200-62356800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr11:62343400-62351600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr11:62343400-62355000	Weak transcription	NHDF-Ad	bronchial
16	chr11:62343400-62355400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr11:62343400-62355800	Strong transcription	Brain Germinal Matrix	brain
18	chr11:62343400-62356200	Strong transcription	Primary T cells from cord blood	blood
19	chr11:62343400-62356600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr11:62343400-62356600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr11:62343400-62356600	Strong transcription	Fetal Thymus	thymus
22	chr11:62343400-62356800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr11:62343600-62356200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr11:62343600-62356600	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr11:62343800-62356800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr11:62344000-62351800	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr11:62344000-62356200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr11:62344200-62356200	Strong transcription	Duodenum Mucosa	Duodenum
29	chr11:62344400-62355000	Weak transcription	HSMMtube	muscle
30	chr11:62344800-62351400	Strong transcription	Placenta	Placenta
31	chr11:62344800-62356200	Strong transcription	Fetal Lung	lung
32	chr11:62344800-62356800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:62344800-62356800	Strong transcription	Fetal Muscle Leg	muscle
34	chr11:62344800-62356800	Strong transcription	Fetal Stomach	stomach
35	chr11:62344800-62358200	Weak transcription	Right Atrium	heart
36	chr11:62345000-62350600	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr11:62345000-62351200	Weak transcription	Fetal Kidney	kidney
38	chr11:62345000-62356800	Strong transcription	Fetal Intestine Large	intestine
39	chr11:62345200-62352800	Weak transcription	Stomach Mucosa	stomach
40	chr11:62345200-62355000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr11:62345200-62355000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr11:62345200-62356800	Strong transcription	Fetal Intestine Small	intestine
43	chr11:62346200-62356600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr11:62346400-62354000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr11:62346400-62354800	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr11:62346400-62356800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr11:62346600-62351000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr11:62346600-62356800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr11:62346600-62358400	Weak transcription	Small Intestine	intestine
50	chr11:62347000-62351200	Weak transcription	Brain Substantia Nigra	brain

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