Variant report

Variant	rs13062429
Chromosome Location	chr3:49559485-49559486
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10212296	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1050088	0.83[ASN][1000 genomes]
rs11130199	0.83[ASN][1000 genomes]
rs11130202	0.83[ASN][1000 genomes]
rs11130203	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11708955	0.84[EUR][1000 genomes]
rs11711485	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11712569	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11713474	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11719996	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11720264	0.83[ASN][1000 genomes]
rs11720597	0.82[EUR][1000 genomes]
rs11926781	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12330269	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12489092	0.83[ASN][1000 genomes]
rs13079082	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13079643	0.82[AMR][1000 genomes]
rs1568661	0.83[ASN][1000 genomes]
rs1801143	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2312461	0.83[ASN][1000 genomes]
rs34196454	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34293138	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34363169	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34427167	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35115732	0.81[AMR][1000 genomes]
rs35261698	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35701831	0.83[ASN][1000 genomes]
rs35999162	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3811697	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3870337	0.83[ASN][1000 genomes]
rs3870338	0.83[ASN][1000 genomes]
rs3877784	0.83[ASN][1000 genomes]
rs3924462	0.83[ASN][1000 genomes]
rs3926569	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4625	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4855836	0.83[ASN][1000 genomes]
rs4855855	0.82[ASN][1000 genomes]
rs4855859	0.83[ASN][1000 genomes]
rs4855861	0.83[ASN][1000 genomes]
rs4855864	0.83[ASN][1000 genomes]
rs67216675	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6766131	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6766581	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6797664	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71324962	0.81[AMR][1000 genomes]
rs71615484	0.85[ASN][1000 genomes]
rs7622302	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7630869	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7633271	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7637999	0.83[ASN][1000 genomes]
rs7643845	0.83[ASN][1000 genomes]
rs7646366	0.82[AMR][1000 genomes]
rs9818590	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9821311	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9827021	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9837027	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9841110	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9850072	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9853683	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9858280	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9858418	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9875617	0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13062429	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs13062429	IHPK2	Cis_1M	lymphoblastoid	RTeQTL
rs13062429	FAM212A	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49529600-49568600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr3:49539600-49568600	Weak transcription	Small Intestine	intestine
3	chr3:49546200-49577000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr3:49547000-49572000	Weak transcription	Fetal Brain Male	brain
5	chr3:49547400-49562200	Strong transcription	Primary T cells from cord blood	blood
6	chr3:49547600-49564200	Strong transcription	Fetal Intestine Small	intestine
7	chr3:49547800-49560400	Strong transcription	Fetal Thymus	thymus
8	chr3:49547800-49562800	Strong transcription	Fetal Stomach	stomach
9	chr3:49548000-49562800	Strong transcription	Fetal Intestine Large	intestine
10	chr3:49548400-49577400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:49549200-49568800	Weak transcription	Osteobl	bone
12	chr3:49550800-49568400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:49551200-49561600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:49551400-49571400	Weak transcription	Stomach Mucosa	stomach
15	chr3:49551400-49572200	Weak transcription	NH-A	brain
16	chr3:49551600-49567600	Weak transcription	K562	blood
17	chr3:49551600-49569400	Weak transcription	Fetal Kidney	kidney
18	chr3:49553800-49568400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:49554000-49567000	Weak transcription	A549	lung
20	chr3:49554000-49567600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:49554400-49568200	Weak transcription	NHDF-Ad	bronchial
22	chr3:49555200-49561000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:49555400-49560200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:49555400-49564000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr3:49555400-49567600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:49555400-49567600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:49555400-49567800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr3:49555400-49568000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr3:49555400-49568200	Weak transcription	NHLF	lung
30	chr3:49555400-49568600	Weak transcription	Fetal Lung	lung
31	chr3:49555600-49567800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:49555800-49568400	Weak transcription	HUVEC	blood vessel
33	chr3:49555800-49572200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr3:49556000-49568000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr3:49556000-49568000	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr3:49556000-49568600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr3:49556200-49560200	Weak transcription	Dnd41	blood
38	chr3:49556200-49567000	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:49556200-49567400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:49556200-49567600	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr3:49556200-49568000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr3:49556400-49560400	Weak transcription	Primary B cells from peripheral blood	blood
43	chr3:49556400-49561600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:49556400-49567800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:49556400-49567800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr3:49556600-49566800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr3:49556600-49567200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr3:49557000-49560200	Weak transcription	Gastric	stomach
49	chr3:49557000-49560800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr3:49557000-49567800	Weak transcription	Primary T cells fromperipheralblood	blood

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