Variant report

Variant	rs905290
Chromosome Location	chr11:8753729-8753730
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8746386..8749043-chr11:8752084..8753832,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166444	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10769947	0.96[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10769948	0.96[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10769955	0.92[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10769957	0.96[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10769958	0.92[CEU][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes]
rs10769967	0.80[CEU][hapmap]
rs10769970	0.80[CEU][hapmap]
rs10769971	1.00[YRI][hapmap]
rs10769973	0.80[CEU][hapmap]
rs10840114	1.00[YRI][hapmap]
rs10840130	1.00[YRI][hapmap]
rs10840134	0.83[CEU][hapmap]
rs10840141	0.80[CEU][hapmap]
rs10840142	0.80[CEU][hapmap]
rs10840148	0.80[CEU][hapmap]
rs11042055	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11042059	0.96[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11042060	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11042067	0.81[AMR][1000 genomes]
rs11042069	0.96[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11042103	0.80[CEU][hapmap]
rs12224436	0.90[CEU][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12421789	0.92[CEU][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes]
rs1529641	0.82[CEU][hapmap]
rs2316865	0.96[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2568061	0.80[CEU][hapmap]
rs2568065	0.80[CEU][hapmap]
rs2568090	0.80[CEU][hapmap]
rs3763918	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3794153	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4579928	0.92[CEU][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes]
rs4910062	1.00[YRI][hapmap]
rs4929911	0.96[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4929912	0.96[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4929914	0.96[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4929916	0.92[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes]
rs6484484	0.92[CEU][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes]
rs7107867	0.82[EUR][1000 genomes]
rs7123429	0.80[CEU][hapmap]
rs7129667	0.82[EUR][1000 genomes]
rs7937298	0.80[CEU][hapmap]
rs7940366	1.00[YRI][hapmap]
rs7944560	0.92[CEU][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes]
rs7945705	0.80[CEU][hapmap]

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs905290	TMEM9B-AS1	cis	lung	GTEx
rs905290	OR52A1	cis	parietal	SCAN
rs905290	ST5	cis	parietal	SCAN
rs905290	OR51B6	cis	parietal	SCAN
rs905290	TMEM9B	cis	parietal	SCAN
rs905290	OR51A7	cis	cerebellum	SCAN
rs905290	RRP8	cis	parietal	SCAN
rs905290	TRIM66	cis	lung	GTEx
rs905290	OR52E8	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8736200-8773800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr11:8742600-8754000	Weak transcription	Hela-S3	cervix
3	chr11:8744000-8754200	Weak transcription	A549	lung
4	chr11:8744200-8757600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr11:8745000-8754400	Weak transcription	Small Intestine	intestine
6	chr11:8745600-8754000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr11:8746000-8754200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr11:8746200-8757400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr11:8746400-8757200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:8746600-8757200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr11:8746600-8783000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:8747800-8756400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr11:8748800-8754600	Weak transcription	Fetal Thymus	thymus
14	chr11:8749000-8754200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr11:8749400-8754400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr11:8749400-8754600	Weak transcription	Fetal Kidney	kidney
17	chr11:8750200-8753800	Strong transcription	Fetal Intestine Small	intestine
18	chr11:8750600-8753800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr11:8750600-8754000	Weak transcription	Psoas Muscle	Psoas
20	chr11:8750800-8760200	Weak transcription	Fetal Brain Male	brain
21	chr11:8751200-8754000	Weak transcription	Brain Angular Gyrus	brain
22	chr11:8751400-8753800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr11:8751600-8754000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr11:8751600-8754000	Weak transcription	Fetal Lung	lung
25	chr11:8751600-8754000	Weak transcription	HepG2	liver
26	chr11:8751600-8754000	Weak transcription	NHEK	skin
27	chr11:8752000-8755800	Enhancers	Right Atrium	heart
28	chr11:8752400-8755200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr11:8752400-8755400	Weak transcription	K562	blood
30	chr11:8752600-8754600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr11:8752600-8755800	Enhancers	Right Ventricle	heart
32	chr11:8752600-8756000	Enhancers	Primary B cells from peripheral blood	blood
33	chr11:8752600-8769800	Weak transcription	Colonic Mucosa	Colon
34	chr11:8752600-8775200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr11:8752800-8754000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr11:8752800-8754000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr11:8752800-8755600	Enhancers	Colon Smooth Muscle	Colon
38	chr11:8752800-8755600	Enhancers	HSMMtube	muscle
39	chr11:8752800-8755800	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr11:8752800-8758600	Enhancers	Left Ventricle	heart
41	chr11:8753000-8753800	Enhancers	Primary B cells from cord blood	blood
42	chr11:8753000-8754000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr11:8753000-8754000	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr11:8753000-8754200	Enhancers	HSMM	muscle
45	chr11:8753000-8754400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr11:8753000-8755200	Enhancers	Adipose Nuclei	Adipose
47	chr11:8753000-8755200	Enhancers	Aorta	Aorta
48	chr11:8753000-8755600	Genic enhancers	Fetal Muscle Leg	muscle
49	chr11:8753000-8755600	Enhancers	Lung	lung
50	chr11:8753000-8755600	Enhancers	Pancreas	Pancrea

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