Variant report

Variant	rs3816492
Chromosome Location	chr11:66297363-66297364
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66296511..66298892-chr11:66305917..66307641,2	MCF-7	breast:
2	chr11:66294722..66297580-chr11:66298960..66300977,3	MCF-7	breast:
3	chr11:66296605..66298813-chr11:66310746..66312650,2	MCF-7	breast:
4	chr11:66280557..66283218-chr11:66296773..66299688,2	MCF-7	breast:
5	chr11:66290316..66295871-chr11:66296274..66298887,5	K562	blood:

Variant related genes	Relation type
ENSG00000174483	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10501397	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10896124	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10896125	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10896129	0.97[EUR][1000 genomes]
rs11227495	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11227497	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11227498	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11227499	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11227500	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11227501	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11227502	1.00[EUR][1000 genomes]
rs11227503	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11227509	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11227510	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11227511	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11227512	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11227514	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11227515	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11227522	0.88[EUR][1000 genomes]
rs11227523	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11227525	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11227527	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11227534	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11537993	1.00[YRI][hapmap]
rs11550057	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs11550299	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11821155	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11822028	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11822099	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11824771	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12099041	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12221821	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12223479	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12272545	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13897	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs15969	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs17065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17147644	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17495838	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17496250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17496586	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17580784	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2075792	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2276406	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2277302	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2279864	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2279865	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs2282529	1.00[YRI][hapmap]
rs2298806	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2305532	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2305533	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2305534	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2305535	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28414721	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3179961	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35166611	1.00[YRI][hapmap]
rs35733139	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3737525	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741360	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3819247	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3825065	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3867132	1.00[YRI][hapmap]
rs3892818	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4542420	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4576	1.00[CEU][hapmap];0.80[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs4630309	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs4930182	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4930183	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4930377	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4930378	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4930379	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4930380	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs519380	1.00[CHB][hapmap];0.92[MEX][hapmap]
rs56144989	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57045447	0.97[EUR][1000 genomes]
rs57207756	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57288351	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs573673	0.82[CHB][hapmap]
rs575797	0.82[CHB][hapmap]
rs57596493	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57634456	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57691879	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57724777	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59829960	0.97[EUR][1000 genomes]
rs59982644	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60358007	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60645853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61561111	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61582507	0.89[EUR][1000 genomes]
rs639938	0.82[CHB][hapmap]
rs645307	0.82[CHB][hapmap]
rs7104378	0.87[EUR][1000 genomes]
rs7116921	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7116940	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7123176	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7928882	0.81[GIH][hapmap];0.85[MEX][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7939759	0.97[EUR][1000 genomes]
rs7943327	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7950407	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7950790	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
2	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3816492	ESRRA	cis	cerebellum	SCAN
rs3816492	SART1	cis	cerebellum	SCAN
rs3816492	SSSCA1	cis	parietal	SCAN
rs3816492	C11orf80	cis	cerebellum	SCAN
rs3816492	CHKA	cis	cerebellum	SCAN
rs3816492	CTSF	cis	cerebellum	SCAN
rs3816492	CCND1	cis	parietal	SCAN
rs3816492	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs3816492	RBM4	cis	cerebellum	SCAN
rs3816492	ASRGL1	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66278600-66311000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:66278800-66309800	Weak transcription	HSMMtube	muscle
3	chr11:66278800-66312800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:66279000-66303000	Weak transcription	Primary B cells from cord blood	blood
5	chr11:66279000-66306200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:66279000-66309200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr11:66279000-66313000	Weak transcription	Small Intestine	intestine
8	chr11:66279200-66309800	Weak transcription	HUVEC	blood vessel
9	chr11:66279200-66310400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr11:66279200-66310800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr11:66279200-66310800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr11:66279400-66311000	Weak transcription	Fetal Brain Male	brain
13	chr11:66279400-66311200	Weak transcription	Right Atrium	heart
14	chr11:66279800-66305200	Strong transcription	Fetal Muscle Leg	muscle
15	chr11:66281000-66311000	Strong transcription	Fetal Stomach	stomach
16	chr11:66282000-66309600	Weak transcription	NHDF-Ad	bronchial
17	chr11:66283400-66312800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr11:66286200-66301000	Strong transcription	Placenta	Placenta
19	chr11:66286200-66301200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr11:66287400-66299200	Weak transcription	HepG2	liver
21	chr11:66289000-66308200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr11:66289000-66309800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr11:66289000-66312800	Weak transcription	Stomach Mucosa	stomach
24	chr11:66290200-66310800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr11:66290800-66302800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr11:66291000-66298600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr11:66291000-66303000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr11:66291000-66309800	Weak transcription	HSMM	muscle
29	chr11:66291200-66302800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr11:66291200-66303200	Weak transcription	Left Ventricle	heart
31	chr11:66291200-66306200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr11:66291200-66309800	Weak transcription	NH-A	brain
33	chr11:66291200-66311600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr11:66291400-66300000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr11:66291400-66303200	Weak transcription	Osteobl	bone
36	chr11:66291400-66304200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr11:66291400-66304400	Weak transcription	Psoas Muscle	Psoas
38	chr11:66291400-66305800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr11:66291400-66305800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr11:66291400-66309400	Weak transcription	A549	lung
41	chr11:66291400-66309600	Weak transcription	GM12878-XiMat	blood
42	chr11:66291400-66311000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:66291600-66299400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr11:66291600-66306200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr11:66291600-66309200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr11:66291600-66309800	Weak transcription	HMEC	breast
47	chr11:66291600-66312600	Weak transcription	NHEK	skin
48	chr11:66292000-66298200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr11:66292000-66303000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr11:66292000-66306200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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