Variant report

Variant	rs34889065
Chromosome Location	chr3:49124817-49124818
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49113907..49116701-chr3:49123584..49125304,2	MCF-7	breast:
2	chr3:49124027..49128766-chr3:49129255..49132743,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198218	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10154895	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10865954	0.85[ASN][1000 genomes]
rs11130184	0.82[ASN][1000 genomes]
rs11552724	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706052	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11706189	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11710247	0.81[EUR][1000 genomes]
rs11712006	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713297	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11715581	0.82[ASN][1000 genomes]
rs11716334	0.82[ASN][1000 genomes]
rs11716614	0.81[AMR][1000 genomes]
rs11717978	0.81[EUR][1000 genomes]
rs11718982	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11719220	0.81[EUR][1000 genomes]
rs11719457	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12487580	0.80[ASN][1000 genomes]
rs12490393	0.82[ASN][1000 genomes]
rs12493001	0.89[ASN][1000 genomes]
rs12629759	0.82[ASN][1000 genomes]
rs12636030	0.89[ASN][1000 genomes]
rs12637037	0.80[ASN][1000 genomes]
rs12637576	0.82[ASN][1000 genomes]
rs13064784	0.95[ASN][1000 genomes]
rs13072554	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13080725	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13086240	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13087930	0.85[EUR][1000 genomes]
rs13090839	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13096406	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3212	0.95[ASN][1000 genomes]
rs34326553	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34477108	0.80[EUR][1000 genomes]
rs34504524	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34509487	0.85[EUR][1000 genomes]
rs34566463	0.81[EUR][1000 genomes]
rs34580506	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35060561	0.81[EUR][1000 genomes]
rs35102816	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35108630	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35283189	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35673421	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3923475	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4279134	0.95[ASN][1000 genomes]
rs4308307	0.82[ASN][1000 genomes]
rs4364202	0.93[ASN][1000 genomes]
rs4499638	0.87[ASN][1000 genomes]
rs4513485	0.95[ASN][1000 genomes]
rs4521268	0.95[ASN][1000 genomes]
rs4536858	0.87[ASN][1000 genomes]
rs4955410	0.85[ASN][1000 genomes]
rs4955418	0.87[ASN][1000 genomes]
rs4955419	0.82[ASN][1000 genomes]
rs4955420	0.82[ASN][1000 genomes]
rs5030795	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55713230	0.87[ASN][1000 genomes]
rs56004653	0.81[AMR][1000 genomes]
rs56318350	0.85[EUR][1000 genomes]
rs61583136	0.85[ASN][1000 genomes]
rs61729488	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62262517	0.93[ASN][1000 genomes]
rs66991555	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6770112	0.85[ASN][1000 genomes]
rs6779394	1.00[ASN][1000 genomes]
rs6784111	0.89[ASN][1000 genomes]
rs6790914	0.87[ASN][1000 genomes]
rs6794924	0.82[ASN][1000 genomes]
rs6795025	0.87[ASN][1000 genomes]
rs71324929	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73082362	0.81[AMR][1000 genomes]
rs7615235	0.87[ASN][1000 genomes]
rs7626445	0.95[ASN][1000 genomes]
rs9814987	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9835439	0.89[ASN][1000 genomes]
rs9837237	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9837625	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9840050	0.95[ASN][1000 genomes]
rs9846123	0.82[ASN][1000 genomes]
rs9855123	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9862483	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9880088	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv876765	chr3:49119063-49160671	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs34889065	WDR6	cis	Adipose Subcutaneous	GTEx
rs34889065	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs34889065	WDR6	cis	Artery Tibial	GTEx
rs34889065	WDR6	cis	Esophagus Mucosa	GTEx
rs34889065	WDR6	cis	Whole Blood	GTEx
rs34889065	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs34889065	WDR6	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49066800-49130000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:49066800-49130200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:49094600-49128200	Weak transcription	Fetal Brain Male	brain
4	chr3:49095400-49129600	Weak transcription	Stomach Mucosa	stomach
5	chr3:49109000-49126200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:49111800-49129600	Weak transcription	HSMMtube	muscle
7	chr3:49113800-49128400	Weak transcription	Small Intestine	intestine
8	chr3:49113800-49129200	Weak transcription	Psoas Muscle	Psoas
9	chr3:49114400-49125600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:49114400-49126000	Weak transcription	Ovary	ovary
11	chr3:49114400-49126200	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:49114400-49126200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:49114400-49128600	Weak transcription	NHLF	lung
14	chr3:49114400-49129600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr3:49114400-49129600	Weak transcription	Right Ventricle	heart
16	chr3:49114400-49129800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:49114400-49130000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:49114800-49129400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:49115000-49125800	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:49115000-49127400	Weak transcription	Brain Substantia Nigra	brain
21	chr3:49115000-49128000	Weak transcription	Pancreas	Pancrea
22	chr3:49115000-49129200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:49115000-49130200	Weak transcription	Aorta	Aorta
24	chr3:49115000-49130600	Weak transcription	Spleen	Spleen
25	chr3:49115200-49126600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:49115200-49127000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:49115200-49129400	Weak transcription	Fetal Brain Female	brain
28	chr3:49115200-49129600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:49115600-49126000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:49115600-49126800	Weak transcription	Brain Angular Gyrus	brain
31	chr3:49115600-49126800	Weak transcription	A549	lung
32	chr3:49115600-49128800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:49115600-49128800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:49115600-49129400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:49115600-49129600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr3:49115600-49129600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr3:49115600-49130000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:49115600-49130200	Weak transcription	Esophagus	oesophagus
39	chr3:49115800-49126800	Weak transcription	Hela-S3	cervix
40	chr3:49115800-49126800	Weak transcription	HepG2	liver
41	chr3:49115800-49126800	Weak transcription	HUVEC	blood vessel
42	chr3:49115800-49126800	Weak transcription	Osteobl	bone
43	chr3:49115800-49127000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr3:49115800-49128000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:49115800-49128200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:49115800-49129600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr3:49115800-49129600	Weak transcription	K562	blood
48	chr3:49116000-49126800	Weak transcription	NH-A	brain
49	chr3:49116000-49128000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:49116000-49128200	Weak transcription	Stomach Smooth Muscle	stomach

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