Variant report

Variant	rs7942154
Chromosome Location	chr11:62337163-62337164
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:62318888..62321035-chr11:62336105..62338398,2	K562	blood:
2	chr11:62313891..62315572-chr11:62335092..62338031,2	K562	blood:
3	chr11:62335812..62337600-chr11:62494575..62496814,2	MCF-7	breast:
4	chr11:62310701..62316525-chr11:62336307..62345701,21	MCF-7	breast:
5	chr11:62336008..62338015-chr11:62571468..62573049,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257058	Chromatin interaction
ENSG00000234857	Chromatin interaction
ENSG00000214753	Chromatin interaction
ENSG00000124942	Chromatin interaction
ENSG00000162222	Chromatin interaction
ENSG00000162231	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1061093	1.00[ASN][1000 genomes]
rs11231137	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11231138	0.97[ASN][1000 genomes]
rs11231141	1.00[ASN][1000 genomes]
rs11231144	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11231145	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11231150	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11231151	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11231152	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11231154	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11231156	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12049914	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12223627	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12225213	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12226821	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17773169	0.93[ASN][1000 genomes]
rs2428551	0.90[ASN][1000 genomes]
rs2516633	0.90[EUR][1000 genomes]
rs34065644	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35587183	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35880596	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs58720921	0.90[ASN][1000 genomes]
rs60098285	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61296092	1.00[ASN][1000 genomes]
rs67308910	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7124057	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71490390	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71490392	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs71490394	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs72927213	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs72927237	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7928833	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7930896	0.80[AFR][1000 genomes]
rs7937146	0.90[ASN][1000 genomes]
rs7942991	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7943191	0.83[AMR][1000 genomes];1.00[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	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	nsv347	chr11:62297068-62338927	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active 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	65 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7942154	MTA2	cis	Esophagus Mucosa	GTEx
rs7942154	EEF1G	cis	multi-tissue	Pritchard
rs7942154	EML3	cis	Whole Blood	GTEx
rs7942154	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	chr11:62322400-62340000	Strong transcription	Fetal Brain Female	brain
2	chr11:62324800-62338800	Strong transcription	Brain Germinal Matrix	brain
3	chr11:62324800-62339600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr11:62325000-62338600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:62325000-62338800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr11:62325200-62339600	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr11:62326400-62339200	Strong transcription	Fetal Thymus	thymus
8	chr11:62326800-62337400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr11:62328400-62338800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:62328600-62337800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr11:62328600-62338800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr11:62328600-62338800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr11:62328600-62339200	Strong transcription	Brain Hippocampus Middle	brain
14	chr11:62328600-62339400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr11:62328600-62339600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr11:62328600-62339800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:62328600-62340200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr11:62328800-62338600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr11:62328800-62339000	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr11:62328800-62339800	Strong transcription	Stomach Smooth Muscle	stomach
21	chr11:62329000-62337200	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr11:62329000-62338800	Strong transcription	Fetal Muscle Leg	muscle
23	chr11:62329000-62339800	Strong transcription	Fetal Muscle Trunk	muscle
24	chr11:62329200-62339400	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr11:62329600-62339400	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr11:62329600-62339800	Strong transcription	Primary B cells from peripheral blood	blood
27	chr11:62329800-62338000	Strong transcription	Fetal Stomach	stomach
28	chr11:62329800-62339000	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr11:62329800-62339400	Strong transcription	Lung	lung
30	chr11:62330000-62338600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr11:62330000-62339200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr11:62330000-62339200	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr11:62330000-62339600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
34	chr11:62330200-62338800	Strong transcription	Spleen	Spleen
35	chr11:62330200-62339600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr11:62330400-62338000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr11:62330400-62338600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
38	chr11:62330400-62339000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr11:62330400-62339000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr11:62330400-62339200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr11:62330600-62339800	Strong transcription	Thymus	Thymus
42	chr11:62330800-62338800	Strong transcription	Left Ventricle	heart
43	chr11:62330800-62339400	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr11:62331000-62339200	Strong transcription	Rectal Smooth Muscle	rectum
45	chr11:62331200-62337200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr11:62331200-62339800	Strong transcription	Ovary	ovary
47	chr11:62331400-62339400	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr11:62331600-62337600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:62331600-62338800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr11:62331600-62338800	Strong transcription	HUES6 Cell Line	embryonic stem cell

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