Variant report

Variant	rs7947230
Chromosome Location	chr11:8646670-8646671
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:8644589..8647498-chr11:8659025..8660844,2	MCF-7	breast:
2	chr11:8644859..8647194-chr11:8648029..8650090,2	K562	blood:
3	chr11:8641168..8642878-chr11:8644731..8647505,2	K562	blood:
4	chr11:8645853..8647429-chr11:8659220..8661284,2	K562	blood:
5	chr11:8645312..8647194-chr11:8647433..8649529,2	K562	blood:
6	chr11:8645853..8648717-chr11:8659784..8661524,2	K562	blood:
7	chr11:8524893..8527404-chr11:8645934..8647701,2	K562	blood:

Variant related genes	Relation type
ENSG00000166436	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10160373	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1026021	0.90[GIH][hapmap];1.00[MEX][hapmap]
rs10743073	0.88[GIH][hapmap];0.95[MEX][hapmap]
rs10743084	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10769938	0.94[LWK][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes]
rs11042019	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11042033	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12286011	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12295729	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12295855	0.88[GIH][hapmap];0.90[MEX][hapmap]
rs12787554	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13328833	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16938253	0.86[GIH][hapmap];0.90[MEX][hapmap]
rs2166470	0.93[GIH][hapmap];0.90[MEX][hapmap]
rs34655699	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3942866	1.00[CEU][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57012665	0.88[ASN][1000 genomes]
rs7931834	0.93[GIH][hapmap];0.95[MEX][hapmap]
rs7935453	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751035	chr11:8431654-8685451	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv896983	chr11:8526643-8682465	ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7947230	OR51E2	cis	cerebellum	SCAN
rs7947230	SWAP70	cis	cerebellum	SCAN
rs7947230	SNORA45	cis	cerebellum	SCAN
rs7947230	OR52E2	cis	parietal	SCAN
rs7947230	STK33	cis	cerebellum	SCAN
rs7947230	HBB	cis	cerebellum	SCAN
rs7947230	RPL27A	cis	cerebellum	SCAN
rs7947230	RPL27A	cis	parietal	SCAN
rs7947230	ST5	cis	cerebellum	SCAN
rs7947230	AMPD3	cis	parietal	SCAN
rs7947230	SNORA45	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8626000-8661600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:8626000-8661800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr11:8626200-8653000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr11:8626600-8648800	Weak transcription	Stomach Mucosa	stomach
5	chr11:8626800-8659600	Weak transcription	Hela-S3	cervix
6	chr11:8630600-8653000	Weak transcription	Osteobl	bone
7	chr11:8632800-8659000	Weak transcription	Colon Smooth Muscle	Colon
8	chr11:8632800-8663800	Weak transcription	Fetal Kidney	kidney
9	chr11:8634000-8646800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr11:8634200-8647200	Strong transcription	Liver	Liver
11	chr11:8634600-8661600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr11:8634600-8661800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:8634800-8657600	Weak transcription	Psoas Muscle	Psoas
14	chr11:8635400-8646800	Weak transcription	Fetal Brain Male	brain
15	chr11:8635400-8647000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:8635400-8661400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr11:8635600-8647000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:8636200-8661400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr11:8636600-8657000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr11:8636800-8647000	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr11:8636800-8647200	Strong transcription	Stomach Smooth Muscle	stomach
22	chr11:8636800-8647400	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr11:8637000-8647200	Strong transcription	Fetal Intestine Small	intestine
24	chr11:8637000-8661600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr11:8637000-8703200	Weak transcription	Small Intestine	intestine
26	chr11:8637200-8646800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:8637200-8646800	Strong transcription	Placenta	Placenta
28	chr11:8637200-8646800	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr11:8637200-8647000	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr11:8637200-8647000	Strong transcription	Lung	lung
31	chr11:8637200-8647200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr11:8637200-8647200	Strong transcription	Aorta	Aorta
33	chr11:8637200-8647200	Strong transcription	Pancreas	Pancrea
34	chr11:8637200-8647200	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr11:8637200-8647200	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr11:8637200-8647400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr11:8637200-8647600	Strong transcription	Primary T cells from cord blood	blood
38	chr11:8637200-8647600	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr11:8637200-8648200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr11:8637200-8648800	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr11:8637400-8646800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr11:8637400-8646800	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr11:8637400-8647000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr11:8637400-8647000	Strong transcription	Spleen	Spleen
45	chr11:8637400-8647600	Strong transcription	Adipose Nuclei	Adipose
46	chr11:8637400-8659200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr11:8637600-8646800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr11:8637600-8647000	Strong transcription	Dnd41	blood
49	chr11:8637600-8647400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr11:8637600-8647400	Strong transcription	Fetal Stomach	stomach

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