Variant report

Variant	rs7939226
Chromosome Location	chr11:74304509-74304510
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74303751..74305512-chr11:74357483..74359321,2	MCF-7	breast:
2	chr11:74203150..74205819-chr11:74301632..74306352,4	MCF-7	breast:
3	chr11:74203316..74206013-chr11:74301160..74305311,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254837	Chromatin interaction
ENSG00000175536	Chromatin interaction
ENSG00000077514	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10899012	1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs10899013	0.97[ASN][1000 genomes]
rs11826567	0.83[ASN][1000 genomes]
rs12364155	0.97[ASN][1000 genomes]
rs12801024	0.93[ASN][1000 genomes]
rs34060848	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34222102	0.99[ASN][1000 genomes]
rs34702292	0.97[ASN][1000 genomes]
rs34835838	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35165052	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36005373	0.83[ASN][1000 genomes]
rs3741127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4944925	0.81[MEX][hapmap]
rs61901537	0.97[ASN][1000 genomes]
rs61901538	0.97[ASN][1000 genomes]
rs6592573	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs7106219	0.81[MEX][hapmap]
rs7125480	0.97[ASN][1000 genomes]
rs7932731	0.97[ASN][1000 genomes]
rs7943504	0.83[ASN][1000 genomes]
rs7944514	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs9919663	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv832209	chr11:74155883-74329119	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer 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	30 gene(s)	inside rSNPs	diseases
7	nsv897914	chr11:74266026-74327614	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv897915	chr11:74269817-74327614	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7939226	OR2AT4	cis	parietal	SCAN
rs7939226	SNORD15A	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74302600-74304800	Active TSS	Fetal Kidney	kidney
2	chr11:74302800-74304600	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr11:74302800-74304600	Active TSS	Ovary	ovary
4	chr11:74302800-74304800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr11:74302800-74304800	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr11:74302800-74304800	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr11:74302800-74304800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr11:74302800-74305200	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr11:74303000-74304600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr11:74303000-74304600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:74303000-74304600	Active TSS	Right Ventricle	heart
12	chr11:74303000-74304800	Active TSS	Fetal Intestine Large	intestine
13	chr11:74303000-74304800	Active TSS	Fetal Muscle Trunk	muscle
14	chr11:74303000-74304800	Active TSS	Pancreas	Pancrea
15	chr11:74303000-74304800	Active TSS	Psoas Muscle	Psoas
16	chr11:74303000-74305000	Active TSS	H1 Cell Line	embryonic stem cell
17	chr11:74303000-74305000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr11:74303000-74305200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr11:74303200-74304600	Active TSS	H9 Cell Line	embryonic stem cell
20	chr11:74303200-74304600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr11:74303200-74304600	Active TSS	Brain Substantia Nigra	brain
22	chr11:74303200-74304600	Active TSS	Left Ventricle	heart
23	chr11:74303200-74304600	Active TSS	A549	lung
24	chr11:74303200-74304600	Active TSS	NHDF-Ad	bronchial
25	chr11:74303200-74304800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr11:74303200-74305000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:74303200-74305000	Active TSS	NHLF	lung
28	chr11:74303200-74305200	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr11:74303400-74304600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr11:74303400-74304600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr11:74303400-74304600	Active TSS	Fetal Stomach	stomach
32	chr11:74303400-74304600	Active TSS	Hela-S3	cervix
33	chr11:74303400-74304800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr11:74303400-74304800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr11:74303400-74304800	Active TSS	Muscle Satellite Cultured Cells	--
36	chr11:74303400-74305000	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr11:74303400-74305000	Active TSS	Fetal Brain Female	brain
38	chr11:74303600-74304600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr11:74303600-74304600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:74303600-74304600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr11:74303600-74304600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr11:74303600-74304600	Active TSS	Esophagus	oesophagus
43	chr11:74303600-74304600	Active TSS	Lung	lung
44	chr11:74303600-74304600	Active TSS	Placenta Amnion	Placenta Amnion
45	chr11:74303600-74304600	Active TSS	Small Intestine	intestine
46	chr11:74303600-74304800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr11:74303600-74304800	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr11:74303800-74304800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr11:74304000-74304800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr11:74304000-74304800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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