Variant report

Variant	rs7643845
Chromosome Location	chr3:49530711-49530712
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	chr3:49506988..49509379-chr3:49529279..49532110,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173402	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10212296	0.85[ASN][1000 genomes]
rs1050088	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865955	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130192	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130193	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11130194	0.85[EUR][1000 genomes]
rs11130196	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11130199	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130202	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130203	0.94[ASN][1000 genomes]
rs11130206	0.89[AMR][1000 genomes];0.90[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	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[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[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12489092	0.92[AMR][1000 genomes];0.95[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	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1464566	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1464567	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1464568	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1568661	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1568662	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17595772	0.82[EUR][1000 genomes]
rs17650792	0.82[EUR][1000 genomes]
rs1801143	0.94[ASN][1000 genomes]
rs2117939	0.82[EUR][1000 genomes]
rs2312461	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878298	0.82[EUR][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	0.81[EUR][1000 genomes]
rs35261698	0.94[ASN][1000 genomes]
rs35701831	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35999162	0.90[ASN][1000 genomes]
rs3811697	0.94[ASN][1000 genomes]
rs3870337	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870338	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3877784	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3924462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3924463	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3926569	0.90[ASN][1000 genomes]
rs4241406	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4241408	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4459909	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4625	0.94[ASN][1000 genomes]
rs4855836	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855839	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4855842	0.84[EUR][1000 genomes]
rs4855843	0.83[EUR][1000 genomes]
rs4855855	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4855859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855864	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4855866	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4855873	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4855877	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4955412	0.83[EUR][1000 genomes]
rs55957735	0.85[EUR][1000 genomes]
rs56116382	0.82[ASN][1000 genomes]
rs59152804	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62259939	0.83[EUR][1000 genomes]
rs62261185	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6446274	0.82[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	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6787417	0.83[AFR][1000 genomes]
rs6792911	0.84[EUR][1000 genomes]
rs6797664	0.94[ASN][1000 genomes]
rs6797765	0.83[EUR][1000 genomes]
rs71615484	0.90[ASN][1000 genomes]
rs7371895	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7373849	0.82[EUR][1000 genomes]
rs7621003	0.82[EUR][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	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7637999	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643586	0.85[EUR][1000 genomes]
rs7645445	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs885592	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[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
rs7643845	WDR6	cis	Nerve Tibial	GTEx
rs7643845	WDR6	cis	Muscle Skeletal	GTEx
rs7643845	WDR6	cis	lung	GTEx
rs7643845	WDR6	cis	Adipose Subcutaneous	GTEx
rs7643845	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs7643845	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs7643845	WDR6	cis	Whole Blood	GTEx
rs7643845	AMT	cis	Thyroid	GTEx
rs7643845	WDR6	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49509600-49530800	Weak transcription	Brain Germinal Matrix	brain
2	chr3:49509600-49537800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:49509800-49531000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:49509800-49537600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:49509800-49547800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr3:49510000-49535600	Weak transcription	NHLF	lung
7	chr3:49510000-49547800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:49514400-49532400	Weak transcription	GM12878-XiMat	blood
9	chr3:49514600-49548000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:49514800-49532400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:49515000-49532800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr3:49515000-49535400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr3:49515200-49532400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:49515200-49532400	Weak transcription	Colonic Mucosa	Colon
15	chr3:49515400-49531000	Weak transcription	Gastric	stomach
16	chr3:49515400-49547800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:49515400-49547800	Weak transcription	Fetal Brain Female	brain
18	chr3:49515400-49548800	Weak transcription	Esophagus	oesophagus
19	chr3:49516800-49532400	Weak transcription	Small Intestine	intestine
20	chr3:49516800-49534800	Weak transcription	Liver	Liver
21	chr3:49516800-49537600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:49517000-49547800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:49517200-49547800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:49519400-49530800	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr3:49519400-49535200	Weak transcription	K562	blood
26	chr3:49520400-49532800	Weak transcription	Primary B cells from cord blood	blood
27	chr3:49522200-49530800	Weak transcription	Right Ventricle	heart
28	chr3:49522200-49547800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr3:49522400-49537800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:49522400-49548000	Weak transcription	Spleen	Spleen
31	chr3:49522800-49531600	Weak transcription	Lung	lung
32	chr3:49523200-49531000	Weak transcription	Brain Anterior Caudate	brain
33	chr3:49523400-49531000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:49523400-49531000	Weak transcription	Brain Hippocampus Middle	brain
35	chr3:49523400-49531000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:49523400-49531200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:49523400-49548000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:49523400-49548000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr3:49523600-49530800	Weak transcription	HepG2	liver
40	chr3:49523600-49530800	Weak transcription	Osteobl	bone
41	chr3:49523600-49531000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr3:49523600-49531000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:49523600-49531000	Weak transcription	Ovary	ovary
44	chr3:49523600-49531000	Weak transcription	Pancreas	Pancrea
45	chr3:49523600-49531000	Weak transcription	Psoas Muscle	Psoas
46	chr3:49523600-49531000	Weak transcription	Stomach Mucosa	stomach
47	chr3:49523600-49531000	Weak transcription	NH-A	brain
48	chr3:49523600-49531200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:49523600-49535200	Weak transcription	Fetal Heart	heart
50	chr3:49523600-49535200	Weak transcription	A549	lung

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