Variant report

Variant	rs9888257
Chromosome Location	chr11:9185077-9185078
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	chr11:9182254..9183881-chr11:9184543..9187161,2	K562	blood:
2	chr11:9182922..9186858-chr11:9284240..9287968,3	K562	blood:

Variant related genes	Relation type
ENSG00000184014	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10047438	0.89[ASN][1000 genomes]
rs1039210	0.86[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs10769991	0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs10769995	0.86[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs10769996	0.86[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs10840176	0.82[ASN][1000 genomes]
rs10840178	0.81[ASN][1000 genomes]
rs10840179	0.82[ASN][1000 genomes]
rs10840181	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10840182	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10840183	0.93[ASN][1000 genomes]
rs10840185	0.87[ASN][1000 genomes]
rs10840202	0.90[CHD][hapmap]
rs11042195	0.92[JPT][hapmap]
rs11042199	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11604616	0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs12099067	0.85[CHB][hapmap];0.95[CHD][hapmap]
rs12286943	0.90[CHD][hapmap]
rs1353729	0.82[JPT][hapmap]
rs17256375	0.86[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs1874822	0.84[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1997628	0.83[ASN][1000 genomes]
rs2133217	0.86[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs2291839	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2316088	1.00[CEU][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2647537	0.84[JPT][hapmap]
rs2742556	0.92[JPT][hapmap]
rs4537761	0.90[CHD][hapmap]
rs4627080	0.81[CHD][hapmap]
rs56077948	1.00[ASN][1000 genomes]
rs56216908	0.89[ASN][1000 genomes]
rs7103596	0.85[CHD][hapmap]
rs7109745	0.86[ASN][1000 genomes]
rs7119300	0.81[MEX][hapmap]
rs7123970	0.86[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs7394878	0.86[CHB][hapmap];0.86[CHD][hapmap];0.80[ASN][1000 genomes]
rs7395347	0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs7395846	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs7925308	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs7925418	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7930507	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs7947251	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs883550	0.89[AFR][1000 genomes]
rs956517	0.85[CHB][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1040049	chr11:9152536-9363488	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv526778	chr11:9159739-9185077	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9888257	OR52N2	cis	parietal	SCAN
rs9888257	TRIM5	cis	cerebellum	SCAN
rs9888257	EIF4G2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9155000-9203400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:9161200-9202400	Weak transcription	Small Intestine	intestine
3	chr11:9162000-9191200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr11:9162000-9230600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr11:9166000-9200600	Weak transcription	Colonic Mucosa	Colon
6	chr11:9167800-9187600	Strong transcription	Placenta	Placenta
7	chr11:9169200-9198400	Weak transcription	Thymus	Thymus
8	chr11:9169400-9186400	Weak transcription	Fetal Intestine Small	intestine
9	chr11:9169600-9238000	Weak transcription	Esophagus	oesophagus
10	chr11:9171800-9191400	Weak transcription	Psoas Muscle	Psoas
11	chr11:9171800-9230200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr11:9172000-9230400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr11:9172200-9197800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr11:9172200-9199600	Weak transcription	Gastric	stomach
15	chr11:9173000-9199400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr11:9173400-9191000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr11:9173400-9199600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr11:9173600-9199600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr11:9174000-9194800	Weak transcription	Fetal Kidney	kidney
20	chr11:9174000-9198200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr11:9174000-9199400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr11:9174000-9225800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr11:9174200-9187000	Weak transcription	Fetal Brain Female	brain
24	chr11:9174400-9191000	Weak transcription	Fetal Heart	heart
25	chr11:9175800-9193000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr11:9177800-9187000	Weak transcription	Pancreas	Pancrea
27	chr11:9178200-9195400	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr11:9178600-9190000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr11:9178800-9192200	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr11:9180000-9199600	Weak transcription	Aorta	Aorta
31	chr11:9180800-9191200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:9181400-9186400	Strong transcription	Hela-S3	cervix
33	chr11:9182200-9191800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr11:9182400-9186400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr11:9182400-9187000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr11:9182400-9187200	Weak transcription	Brain Angular Gyrus	brain
37	chr11:9182400-9190400	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr11:9182400-9190800	Weak transcription	Fetal Intestine Large	intestine
39	chr11:9182400-9191200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr11:9182400-9225000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr11:9182400-9231800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr11:9182600-9187000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr11:9182600-9187000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:9182600-9187000	Weak transcription	Brain Germinal Matrix	brain
45	chr11:9182600-9187000	Weak transcription	Right Ventricle	heart
46	chr11:9182600-9187000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr11:9182600-9187000	Weak transcription	Spleen	Spleen
48	chr11:9182600-9187200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr11:9182600-9187200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr11:9182600-9188400	Weak transcription	K562	blood

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