Variant report

Variant	rs3870337
Chromosome Location	chr3:49557095-49557096
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49554866..49557118-chr3:49574115..49576827,2	K562	blood:
2	chr3:49555962..49557496-chr3:49560645..49562383,2	K562	blood:
3	chr3:49551705..49554065-chr3:49554259..49559105,5	K562	blood:
4	chr3:49507807..49509484-chr3:49555798..49559257,3	MCF-7	breast:

Extended variants
information (count: 98 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10212296	0.85[ASN][1000 genomes]
rs1050088	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865955	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130192	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130193	0.86[EUR][1000 genomes]
rs11130194	0.84[EUR][1000 genomes]
rs11130196	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11130199	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130202	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130203	0.94[ASN][1000 genomes]
rs11130206	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11708955	0.82[ASN][1000 genomes]
rs11711485	0.82[ASN][1000 genomes]
rs11712569	0.94[ASN][1000 genomes]
rs11713474	0.86[ASN][1000 genomes]
rs11719996	0.94[ASN][1000 genomes]
rs11720264	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720458	0.92[ASN][1000 genomes]
rs11926781	0.86[ASN][1000 genomes]
rs12330269	0.94[ASN][1000 genomes]
rs12488065	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12489092	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636099	0.83[ASN][1000 genomes]
rs13062429	0.83[ASN][1000 genomes]
rs13079082	0.94[ASN][1000 genomes]
rs13096760	0.87[EUR][1000 genomes]
rs1464566	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1464567	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1464568	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1568661	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1568662	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1801143	0.94[ASN][1000 genomes]
rs2312461	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34196454	0.90[ASN][1000 genomes]
rs34293138	0.94[ASN][1000 genomes]
rs34363169	0.94[ASN][1000 genomes]
rs34427167	0.86[ASN][1000 genomes]
rs34937635	0.80[EUR][1000 genomes]
rs35261698	0.94[ASN][1000 genomes]
rs35701831	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35999162	0.90[ASN][1000 genomes]
rs3811697	0.94[ASN][1000 genomes]
rs3870338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3877784	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3924462	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3924463	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3926569	0.90[ASN][1000 genomes]
rs4241406	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4241408	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4459909	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4625	0.94[ASN][1000 genomes]
rs4855836	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855839	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4855842	0.83[EUR][1000 genomes]
rs4855843	0.83[EUR][1000 genomes]
rs4855855	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4855859	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855861	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855864	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4855866	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4855873	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4855877	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4955412	0.80[EUR][1000 genomes]
rs55957735	0.84[EUR][1000 genomes]
rs56116382	0.82[ASN][1000 genomes]
rs59152804	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62261185	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6446274	0.80[EUR][1000 genomes]
rs67216675	0.82[ASN][1000 genomes]
rs6766131	0.94[ASN][1000 genomes]
rs6766581	0.94[ASN][1000 genomes]
rs6773518	0.83[EUR][1000 genomes]
rs6784820	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6792911	0.82[EUR][1000 genomes]
rs6797664	0.94[ASN][1000 genomes]
rs6797765	0.82[EUR][1000 genomes]
rs71615484	0.90[ASN][1000 genomes]
rs7371895	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7622302	0.94[ASN][1000 genomes]
rs7630869	0.82[ASN][1000 genomes]
rs7631908	0.83[EUR][1000 genomes]
rs7633271	0.94[ASN][1000 genomes]
rs7637665	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7637999	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643586	0.84[EUR][1000 genomes]
rs7643845	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7645445	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs885592	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9818590	0.94[ASN][1000 genomes]
rs9821311	0.84[ASN][1000 genomes]
rs9827021	0.94[ASN][1000 genomes]
rs9837027	0.94[ASN][1000 genomes]
rs9841110	0.82[ASN][1000 genomes]
rs9850072	0.94[ASN][1000 genomes]
rs9853683	0.94[ASN][1000 genomes]
rs9858280	0.90[ASN][1000 genomes]
rs9858418	0.85[ASN][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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3870337	WDR6	cis	Nerve Tibial	GTEx
rs3870337	WDR6	cis	Adipose Subcutaneous	GTEx
rs3870337	WDR6	cis	Artery Tibial	GTEx
rs3870337	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs3870337	WDR6	cis	lung	GTEx
rs3870337	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs3870337	WDR6	cis	Whole Blood	GTEx
rs3870337	AMT	cis	Thyroid	GTEx
rs3870337	WDR6	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	chr3:49547800-49557200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:49547800-49557800	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr3:49547800-49558000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:49547800-49559000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:49547800-49560400	Strong transcription	Fetal Thymus	thymus
12	chr3:49547800-49562800	Strong transcription	Fetal Stomach	stomach
13	chr3:49548000-49562800	Strong transcription	Fetal Intestine Large	intestine
14	chr3:49548400-49577400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr3:49549200-49568800	Weak transcription	Osteobl	bone
16	chr3:49549800-49557400	Strong transcription	Stomach Smooth Muscle	stomach
17	chr3:49550200-49558000	Strong transcription	Duodenum Mucosa	Duodenum
18	chr3:49550600-49558600	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:49550800-49568400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:49551200-49561600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:49551400-49571400	Weak transcription	Stomach Mucosa	stomach
22	chr3:49551400-49572200	Weak transcription	NH-A	brain
23	chr3:49551600-49567600	Weak transcription	K562	blood
24	chr3:49551600-49569400	Weak transcription	Fetal Kidney	kidney
25	chr3:49551800-49557400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:49552200-49558200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:49553000-49558000	Strong transcription	Primary B cells from cord blood	blood
28	chr3:49553000-49558200	Genic enhancers	Left Ventricle	heart
29	chr3:49553200-49559400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:49553600-49558200	Enhancers	Right Atrium	heart
31	chr3:49553800-49568400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:49554000-49557400	Weak transcription	Thymus	Thymus
33	chr3:49554000-49567000	Weak transcription	A549	lung
34	chr3:49554000-49567600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr3:49554200-49558000	Strong transcription	Aorta	Aorta
36	chr3:49554400-49568200	Weak transcription	NHDF-Ad	bronchial
37	chr3:49554600-49557800	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr3:49554800-49558000	Genic enhancers	Placenta	Placenta
39	chr3:49554800-49558000	Enhancers	Psoas Muscle	Psoas
40	chr3:49554800-49558200	Genic enhancers	Pancreas	Pancrea
41	chr3:49554800-49558400	Strong transcription	Esophagus	oesophagus
42	chr3:49554800-49558400	Genic enhancers	Fetal Muscle Leg	muscle
43	chr3:49554800-49559400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:49555000-49557200	Weak transcription	Hela-S3	cervix
45	chr3:49555000-49558200	Genic enhancers	Right Ventricle	heart
46	chr3:49555200-49561000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr3:49555400-49557200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:49555400-49557600	Weak transcription	GM12878-XiMat	blood
49	chr3:49555400-49558400	Enhancers	Liver	Liver
50	chr3:49555400-49560200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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