Variant report

Variant	rs35108630
Chromosome Location	chr3:49088356-49088357
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49088221-49088394	K562	blood:	n/a	n/a
2	POLR2A	chr3:49088108-49088403	K562	blood:	n/a	n/a
3	POLR2A	chr3:49088081-49088423	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49088204..49092295-chr3:49137425..49140867,4	MCF-7	breast:
2	chr3:49087875..49089929-chr3:49090268..49092361,2	K562	blood:

Variant related genes	Relation type
QRICH1	TF binding region
ENSG00000172053	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10154895	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11552724	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11706052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706189	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11708022	0.85[AMR][1000 genomes]
rs11709092	0.81[AMR][1000 genomes]
rs11709246	0.85[AMR][1000 genomes]
rs11710247	0.84[EUR][1000 genomes]
rs11712006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11713297	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11713694	0.85[AMR][1000 genomes]
rs11715689	0.89[AMR][1000 genomes]
rs11715713	0.89[AMR][1000 genomes]
rs11715835	0.85[AMR][1000 genomes]
rs11716614	0.88[AMR][1000 genomes]
rs11717978	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11718982	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11719220	0.84[EUR][1000 genomes]
rs11719457	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11720460	0.81[EUR][1000 genomes]
rs12493001	0.81[ASN][1000 genomes]
rs12636030	0.81[ASN][1000 genomes]
rs12637037	0.92[ASN][1000 genomes]
rs12715434	0.81[EUR][1000 genomes]
rs13064784	0.82[ASN][1000 genomes]
rs13064911	0.82[ASN][1000 genomes]
rs13068038	0.81[EUR][1000 genomes]
rs13072554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13073997	0.85[AMR][1000 genomes]
rs13074318	0.85[AMR][1000 genomes]
rs13080725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084000	0.85[AMR][1000 genomes]
rs13086240	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13087930	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13090839	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13094900	0.82[AMR][1000 genomes]
rs13096406	0.86[EUR][1000 genomes]
rs13316620	0.84[ASN][1000 genomes]
rs3212	0.82[ASN][1000 genomes]
rs34326553	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34477108	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34504524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34509487	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34566463	0.84[EUR][1000 genomes]
rs34580506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34784192	0.81[EUR][1000 genomes]
rs34889065	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35060561	0.84[EUR][1000 genomes]
rs35102816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35185152	0.81[EUR][1000 genomes]
rs35283189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35673421	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3923475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4072859	0.89[ASN][1000 genomes]
rs4279134	0.82[ASN][1000 genomes]
rs4364202	0.80[ASN][1000 genomes]
rs4513485	0.82[ASN][1000 genomes]
rs4521268	0.82[ASN][1000 genomes]
rs4974080	0.85[ASN][1000 genomes]
rs5030795	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56004653	0.88[AMR][1000 genomes]
rs56318350	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61729488	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62262517	0.80[ASN][1000 genomes]
rs6414613	0.85[ASN][1000 genomes]
rs6446196	0.84[ASN][1000 genomes]
rs6446198	0.82[ASN][1000 genomes]
rs6446205	0.85[ASN][1000 genomes]
rs66991555	0.86[EUR][1000 genomes]
rs67060340	0.82[AMR][1000 genomes]
rs67286839	0.81[EUR][1000 genomes]
rs67332931	0.85[AMR][1000 genomes]
rs6779394	0.87[ASN][1000 genomes]
rs6781790	0.85[ASN][1000 genomes]
rs6784111	0.81[ASN][1000 genomes]
rs6789285	0.89[ASN][1000 genomes]
rs6795025	1.00[ASN][1000 genomes]
rs71324924	0.85[AMR][1000 genomes]
rs71324929	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71324939	0.82[EUR][1000 genomes]
rs73082362	0.88[AMR][1000 genomes]
rs7373790	0.92[ASN][1000 genomes]
rs7430198	0.82[ASN][1000 genomes]
rs7432989	0.90[ASN][1000 genomes]
rs7615235	0.90[ASN][1000 genomes]
rs7626445	0.82[ASN][1000 genomes]
rs7639332	0.82[ASN][1000 genomes]
rs8926	0.90[ASN][1000 genomes]
rs9814987	0.85[EUR][1000 genomes]
rs9826525	0.81[EUR][1000 genomes]
rs9828310	0.81[EUR][1000 genomes]
rs9835439	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9837237	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9837625	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9840050	0.82[ASN][1000 genomes]
rs9846123	0.95[ASN][1000 genomes]
rs9847839	0.81[EUR][1000 genomes]
rs9850917	0.81[EUR][1000 genomes]
rs9855123	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9862483	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9880088	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9990153	0.81[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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs35108630	WDR6	cis	Whole Blood	GTEx
rs35108630	WDR6	cis	Esophagus Mucosa	GTEx
rs35108630	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs35108630	WDR6	cis	Artery Tibial	GTEx
rs35108630	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs35108630	WDR6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:127 , 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	chr3:49067200-49116600	Weak transcription	Right Atrium	heart
4	chr3:49067200-49117200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:49067400-49090000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:49067400-49096000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:49067400-49117200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:49067400-49117200	Strong transcription	Fetal Thymus	thymus
9	chr3:49067400-49117400	Strong transcription	Fetal Intestine Small	intestine
10	chr3:49067400-49117400	Strong transcription	Fetal Stomach	stomach
11	chr3:49067400-49117800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:49067400-49118400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:49067600-49095800	Strong transcription	Dnd41	blood
14	chr3:49067600-49097000	Strong transcription	Fetal Muscle Trunk	muscle
15	chr3:49067600-49117200	Strong transcription	Thymus	Thymus
16	chr3:49067600-49117600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:49067800-49117400	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:49070800-49117000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:49072400-49094200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:49073400-49118200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr3:49074200-49096000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr3:49077400-49117200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:49078800-49091200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:49082600-49091800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:49084400-49088600	Weak transcription	K562	blood
26	chr3:49084400-49094000	Weak transcription	Psoas Muscle	Psoas
27	chr3:49084600-49088400	Weak transcription	Pancreas	Pancrea
28	chr3:49084600-49088800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:49084600-49089000	Weak transcription	Fetal Lung	lung
30	chr3:49084600-49089200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:49084600-49089200	Weak transcription	Aorta	Aorta
32	chr3:49084600-49089400	Weak transcription	Fetal Brain Male	brain
33	chr3:49084600-49091000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr3:49084600-49091000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:49084600-49091200	Weak transcription	Fetal Kidney	kidney
36	chr3:49084600-49091400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr3:49084600-49093800	Weak transcription	Stomach Mucosa	stomach
38	chr3:49084600-49094000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:49084600-49094000	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr3:49084600-49110800	Weak transcription	Fetal Heart	heart
41	chr3:49084600-49117200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:49084800-49088400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:49084800-49088600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr3:49084800-49088600	Weak transcription	NH-A	brain
45	chr3:49084800-49088600	Weak transcription	NHDF-Ad	bronchial
46	chr3:49084800-49088800	Weak transcription	Colonic Mucosa	Colon
47	chr3:49084800-49089200	Weak transcription	Brain Substantia Nigra	brain
48	chr3:49084800-49089200	Weak transcription	HMEC	breast
49	chr3:49084800-49089200	Weak transcription	HSMMtube	muscle
50	chr3:49084800-49094200	Weak transcription	Small Intestine	intestine

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