Variant report

Variant	rs13090388
Chromosome Location	chr3:49391082-49391083
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	chr3:49376682..49378615-chr3:49390504..49394214,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114316	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1050450	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10640	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11706370	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11711485	0.89[AMR][1000 genomes]
rs11711536	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712569	0.80[AMR][1000 genomes]
rs11713474	0.81[AMR][1000 genomes]
rs11715915	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11716974	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11719996	0.83[AMR][1000 genomes]
rs11922013	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12330269	0.83[AMR][1000 genomes]
rs13079082	0.82[AMR][1000 genomes]
rs13079643	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13086611	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13087851	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17080528	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17595772	0.94[ASN][1000 genomes]
rs17650792	0.94[ASN][1000 genomes]
rs1800668	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1801143	0.82[AMR][1000 genomes]
rs1987628	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2117939	0.90[ASN][1000 genomes]
rs2878298	0.94[ASN][1000 genomes]
rs34196454	0.80[AMR][1000 genomes]
rs34293138	0.83[AMR][1000 genomes]
rs34363169	0.83[AMR][1000 genomes]
rs34588335	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35115732	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35169793	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35261698	0.85[AMR][1000 genomes]
rs3811697	0.81[AMR][1000 genomes]
rs3811699	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3926569	0.82[AMR][1000 genomes]
rs4625	0.82[AMR][1000 genomes]
rs4955412	0.94[ASN][1000 genomes]
rs4955438	0.82[ASN][1000 genomes]
rs62259939	0.94[ASN][1000 genomes]
rs62259942	0.83[ASN][1000 genomes]
rs6446264	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446272	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6446277	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67216675	0.89[AMR][1000 genomes]
rs67485053	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6766131	0.85[AMR][1000 genomes]
rs6766581	0.83[AMR][1000 genomes]
rs6779524	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6792911	0.82[ASN][1000 genomes]
rs6793308	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797664	0.83[AMR][1000 genomes]
rs6797765	0.94[ASN][1000 genomes]
rs6809216	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6997	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71324962	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7373849	0.87[ASN][1000 genomes]
rs7621003	0.94[ASN][1000 genomes]
rs7622302	0.81[AMR][1000 genomes]
rs7623659	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631908	0.88[ASN][1000 genomes]
rs7633271	0.82[AMR][1000 genomes]
rs7643586	0.82[ASN][1000 genomes]
rs7646366	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7648841	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814873	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9818590	0.85[AMR][1000 genomes]
rs9821311	0.85[AMR][1000 genomes]
rs9827021	0.85[AMR][1000 genomes]
rs9837027	0.81[AMR][1000 genomes]
rs9841110	0.89[AMR][1000 genomes]
rs9850072	0.83[AMR][1000 genomes]
rs9853683	0.83[AMR][1000 genomes]
rs9858280	0.81[AMR][1000 genomes]
rs9858418	0.82[AMR][1000 genomes]
rs9859556	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9871380	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9878943	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13090388	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs13090388	FAM212A	cis	Muscle Skeletal	GTEx
rs13090388	IHPK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49378600-49392000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr3:49379000-49392000	Weak transcription	Left Ventricle	heart
3	chr3:49379800-49392800	Weak transcription	Thymus	Thymus
4	chr3:49381600-49393000	Weak transcription	Right Atrium	heart
5	chr3:49383000-49393600	Weak transcription	Primary T cells from cord blood	blood
6	chr3:49383200-49391800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:49383200-49392400	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:49383400-49391400	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr3:49384600-49392000	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:49384600-49392400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:49384800-49391800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:49387000-49393000	Weak transcription	Aorta	Aorta
13	chr3:49387200-49391400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:49387200-49392800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:49387400-49392800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:49387400-49393000	Weak transcription	Right Ventricle	heart
17	chr3:49387400-49393800	Weak transcription	Gastric	stomach
18	chr3:49387800-49393000	Weak transcription	Dnd41	blood
19	chr3:49388000-49391400	Enhancers	GM12878-XiMat	blood
20	chr3:49388400-49392600	Weak transcription	Lung	lung
21	chr3:49388400-49393000	Weak transcription	Colonic Mucosa	Colon
22	chr3:49388800-49393600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:49389000-49392800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr3:49389200-49394600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:49389400-49391800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:49389400-49391800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:49389400-49392600	Weak transcription	Fetal Lung	lung
28	chr3:49389400-49392800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:49389400-49392800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:49389400-49392800	Weak transcription	Brain Hippocampus Middle	brain
31	chr3:49389400-49392800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:49389400-49393000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr3:49389400-49393600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:49389400-49393800	Weak transcription	Brain Angular Gyrus	brain
35	chr3:49389400-49393800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:49389400-49393800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:49389400-49393800	Weak transcription	Psoas Muscle	Psoas
38	chr3:49389400-49393800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr3:49389600-49392600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr3:49389600-49392800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:49389600-49393000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:49389600-49393600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:49389600-49393600	Weak transcription	Brain Substantia Nigra	brain
44	chr3:49389600-49393800	Weak transcription	Small Intestine	intestine
45	chr3:49389800-49391800	Weak transcription	Colon Smooth Muscle	Colon
46	chr3:49389800-49392200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:49389800-49392200	Weak transcription	Fetal Stomach	stomach
48	chr3:49389800-49392400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:49389800-49392800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:49389800-49392800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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