Variant report

Variant	rs11706370
Chromosome Location	chr3:49441091-49441092
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	chr3:49439336..49441166-chr3:49447994..49450306,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067560	Chromatin interaction
ENSG00000145022	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10212296	0.82[AMR][1000 genomes]
rs1050088	1.00[JPT][hapmap]
rs1050450	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865955	1.00[JPT][hapmap]
rs11130192	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11130193	0.83[ASN][1000 genomes]
rs11130196	0.82[ASN][1000 genomes]
rs11130199	1.00[JPT][hapmap]
rs11711485	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11711536	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11712569	0.85[AMR][1000 genomes]
rs11713474	0.82[AMR][1000 genomes]
rs11715915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11719996	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11720264	1.00[JPT][hapmap]
rs11922013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11926781	0.83[AMR][1000 genomes]
rs12330269	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12489092	1.00[JPT][hapmap]
rs13079082	0.83[AMR][1000 genomes]
rs13079643	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13086611	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13087851	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13090388	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1464566	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1464567	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1464568	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1568661	1.00[JPT][hapmap]
rs17080528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17650792	1.00[JPT][hapmap]
rs1800668	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1801143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs1987628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34196454	0.85[AMR][1000 genomes]
rs34293138	0.85[AMR][1000 genomes]
rs34363169	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34427167	0.83[AMR][1000 genomes]
rs34588335	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34937635	0.87[ASN][1000 genomes]
rs35115732	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35169793	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35261698	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35701831	1.00[JPT][hapmap]
rs35999162	0.82[AMR][1000 genomes]
rs3811697	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs3811699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3870338	1.00[JPT][hapmap]
rs3924462	1.00[JPT][hapmap]
rs3926569	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4459909	0.94[ASN][1000 genomes]
rs4625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs4855839	1.00[JPT][hapmap]
rs4855842	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4855843	0.83[ASN][1000 genomes]
rs4855859	1.00[JPT][hapmap]
rs4855864	1.00[JPT][hapmap]
rs4855873	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4855877	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs55957735	0.92[ASN][1000 genomes]
rs6446264	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6446272	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446274	0.87[ASN][1000 genomes]
rs6446277	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67216675	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67485053	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6766131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6766581	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6779524	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782577	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs6784820	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6792911	0.86[ASN][1000 genomes]
rs6793308	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6797664	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6809216	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71324962	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7622302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7623659	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7630869	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7633271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes]
rs7637999	1.00[JPT][hapmap]
rs7643586	0.86[ASN][1000 genomes]
rs7646366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7648841	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs885592	1.00[JPT][hapmap]
rs9811982	1.00[CEU][hapmap]
rs9814873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9818590	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9821311	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9827021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9837027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs9841110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9850072	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9853683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9858280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs9858418	0.83[AMR][1000 genomes]
rs9859556	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9871380	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs9878943	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11706370	FAM212A	cis	Muscle Skeletal	GTEx
rs11706370	IHPK2	Cis_1M	lymphoblastoid	RTeQTL
rs11706370	RBM6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49399000-49448000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49406000-49445200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:49413200-49441400	Weak transcription	Aorta	Aorta
4	chr3:49413200-49443000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:49413200-49447400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:49422200-49443000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:49424200-49443400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:49426000-49444000	Weak transcription	Esophagus	oesophagus
9	chr3:49426200-49443000	Weak transcription	NHLF	lung
10	chr3:49427000-49448400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:49429000-49441800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:49429000-49447200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:49431200-49447200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:49433800-49444000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:49433800-49447200	Weak transcription	Colonic Mucosa	Colon
16	chr3:49434200-49442800	Weak transcription	Brain Germinal Matrix	brain
17	chr3:49434800-49443000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:49435400-49441200	Weak transcription	Stomach Mucosa	stomach
19	chr3:49435400-49442400	Strong transcription	Fetal Intestine Small	intestine
20	chr3:49435400-49445600	Weak transcription	Fetal Brain Male	brain
21	chr3:49435400-49447000	Weak transcription	HSMMtube	muscle
22	chr3:49435400-49447800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:49435600-49443000	Weak transcription	NHDF-Ad	bronchial
24	chr3:49435600-49443200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:49435800-49443000	Weak transcription	Small Intestine	intestine
26	chr3:49435800-49446800	Weak transcription	Brain Angular Gyrus	brain
27	chr3:49436600-49443200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:49436800-49441800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:49437000-49441400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:49437600-49441800	Strong transcription	Thymus	Thymus
31	chr3:49437800-49441400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:49438000-49441200	Strong transcription	Dnd41	blood
33	chr3:49438000-49441600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
34	chr3:49438000-49441600	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr3:49438000-49442000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:49438200-49441200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:49438200-49441400	Weak transcription	Pancreas	Pancrea
38	chr3:49438200-49441600	Weak transcription	Ovary	ovary
39	chr3:49438200-49442800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:49438200-49443000	Weak transcription	Liver	Liver
41	chr3:49438200-49443800	Weak transcription	K562	blood
42	chr3:49438200-49444000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:49438200-49446800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:49438400-49441600	Strong transcription	Fetal Thymus	thymus
45	chr3:49438600-49441200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:49438600-49441600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:49438600-49441600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:49438600-49441600	Strong transcription	HMEC	breast
49	chr3:49438800-49441600	Strong transcription	Fetal Muscle Leg	muscle
50	chr3:49438800-49441600	Strong transcription	NHEK	skin

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