Variant report

Variant	rs6772452
Chromosome Location	chr3:49040462-49040463
allele	A/G
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	chr3:49037909-49040784	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:49040302-49040520	GM12878	blood:	n/a	n/a
3	FOXA1	chr3:49040246-49040595	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:49040277-49040481	MCF-7	breast:	n/a	n/a
5	POLR2A	chr3:49036309-49042120	K562	blood:	n/a	n/a

Variant related genes	Relation type
WDR6	TF binding region

Extended variants
information (count: 91 )
Associated
traits (count: 35 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10780033	0.89[ASW][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap]
rs10865954	0.84[ASW][hapmap]
rs11130176	0.89[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap]
rs11130181	0.85[EUR][1000 genomes]
rs11130183	0.82[CEU][hapmap]
rs1134591	0.89[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap]
rs11707968	0.90[EUR][1000 genomes]
rs11920534	0.89[ASW][hapmap]
rs12493289	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12637037	0.92[AFR][1000 genomes]
rs12715430	0.88[EUR][1000 genomes]
rs13092715	0.89[ASW][hapmap];0.93[LWK][hapmap]
rs13099075	0.91[EUR][1000 genomes]
rs13315711	0.93[YRI][hapmap]
rs3087866	0.91[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3212	0.89[ASW][hapmap];0.93[LWK][hapmap];0.93[YRI][hapmap]
rs4279134	1.00[ASW][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap]
rs4292260	0.95[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs4513485	0.89[ASW][hapmap]
rs4521268	0.89[ASW][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap]
rs4955410	0.89[ASW][hapmap]
rs4955411	0.95[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs4955416	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs4955420	0.84[ASW][hapmap]
rs4955426	0.95[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs4974079	0.82[LWK][hapmap];0.86[YRI][hapmap]
rs4974080	0.89[LWK][hapmap];0.84[MKK][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs4974081	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4974082	0.89[ASW][hapmap]
rs4974083	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs4974085	0.89[ASW][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap]
rs4974087	0.82[LWK][hapmap];0.86[YRI][hapmap]
rs4974088	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs62259536	0.83[EUR][1000 genomes]
rs6414613	1.00[ASW][hapmap];0.96[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs6414614	0.91[EUR][1000 genomes]
rs6446196	0.80[LWK][hapmap];0.85[YRI][hapmap]
rs6446200	0.88[EUR][1000 genomes]
rs6446204	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs6446205	0.87[LWK][hapmap];0.89[YRI][hapmap]
rs6446247	0.89[EUR][1000 genomes]
rs6446252	0.85[YRI][hapmap]
rs6446253	1.00[YRI][hapmap]
rs6446256	0.85[CEU][hapmap]
rs6779394	0.82[LWK][hapmap];0.86[YRI][hapmap]
rs6781790	0.89[ASW][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs6784111	1.00[JPT][hapmap]
rs6787808	1.00[CEU][hapmap]
rs6789285	0.85[AFR][1000 genomes]
rs6798112	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7100	0.91[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7372883	0.85[EUR][1000 genomes]
rs7373072	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7429661	0.82[CEU][hapmap]
rs7430198	0.82[LWK][hapmap];0.82[YRI][hapmap]
rs7430501	0.89[ASW][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap]
rs7431710	0.89[ASW][hapmap]
rs7431857	0.89[ASW][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap]
rs7432989	0.80[LWK][hapmap];0.86[YRI][hapmap]
rs7434187	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7621015	0.89[ASW][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap]
rs7621226	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7621347	0.85[EUR][1000 genomes]
rs7623023	0.89[ASW][hapmap]
rs7626445	0.89[ASW][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap]
rs7628719	0.89[ASW][hapmap]
rs7643368	0.89[ASW][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap]
rs7649458	1.00[ASW][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs7653408	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs8926	0.87[AFR][1000 genomes]
rs9284885	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs9311430	0.89[ASW][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap]
rs9311431	1.00[CEU][hapmap]
rs9311433	0.89[ASW][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap]
rs9311434	0.89[ASW][hapmap]
rs9637481	0.82[YRI][hapmap]
rs9682444	0.86[YRI][hapmap]
rs9755490	0.81[LWK][hapmap];0.86[YRI][hapmap]
rs9810318	0.90[EUR][1000 genomes]
rs9834003	0.82[CEU][hapmap]
rs9835307	0.82[LWK][hapmap];0.86[YRI][hapmap]
rs9840050	0.89[ASW][hapmap];0.89[LWK][hapmap];0.93[YRI][hapmap]
rs9841640	0.80[AFR][1000 genomes]
rs9846123	1.00[ASW][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs9850134	0.89[ASW][hapmap];0.93[LWK][hapmap];0.93[YRI][hapmap]
rs9864243	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs9865051	0.95[CEU][hapmap];0.90[TSI][hapmap]
rs9876848	0.82[LWK][hapmap];0.86[YRI][hapmap]
rs9879978	1.00[CEU][hapmap]
rs9884022	0.92[YRI][hapmap]

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:35)

SNP	Gene	Cis/trans	Tissue	Source
rs6772452	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs6772452	WDR6	cis	lung	GTEx
rs6772452	AMT	cis	parietal	SCAN
rs6772452	AMT	cis	cerebellum	SCAN
rs6772452	DALRD3	cis	cerebellum	SCAN
rs6772452	LZTFL1	cis	cerebellum	SCAN
rs6772452	AMT	cis	Adipose Subcutaneous	GTEx
rs6772452	NICN1	cis	cerebellum	SCAN
rs6772452	IQCF1	cis	cerebellum	SCAN
rs6772452	QRICH1	cis	cerebellum	SCAN
rs6772452	TLR9	cis	parietal	SCAN
rs6772452	AMT	cis	Nerve Tibial	GTEx
rs6772452	AMT	cis	lung	GTEx
rs6772452	WDR6	cis	parietal	SCAN
rs6772452	AMT	cis	Artery Aorta	GTEx
rs6772452	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs6772452	NICN1	cis	parietal	SCAN
rs6772452	NCKIPSD	cis	Nerve Tibial	GTEx
rs6772452	PHF7	cis	parietal	SCAN
rs6772452	AMT	cis	Thyroid	GTEx
rs6772452	WDR6	cis	Muscle Skeletal	GTEx
rs6772452	GPX1	cis	parietal	SCAN
rs6772452	NICN1-AS1	cis	Thyroid	GTEx
rs6772452	NCKIPSD	cis	parietal	SCAN
rs6772452	ZNF589	cis	parietal	SCAN
rs6772452	NICN1	cis	Thyroid	GTEx
rs6772452	AMT	cis	Artery Tibial	GTEx
rs6772452	WDR6	cis	Nerve Tibial	GTEx
rs6772452	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs6772452	WDR6	cis	lymphoblastoid	seeQTL
rs6772452	AMT	cis	lymphoblastoid	seeQTL
rs6772452	P4HTM	cis	parietal	SCAN
rs6772452	AMT	cis	Whole Blood	GTEx
rs6772452	WDR6	cis	cerebellum	SCAN
rs6772452	DALRD3	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49028800-49043600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:49029000-49043600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:49029000-49043800	Weak transcription	Primary B cells from cord blood	blood
4	chr3:49029200-49043400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:49029200-49043400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:49029400-49041600	Weak transcription	Liver	Liver
7	chr3:49029400-49043400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:49029400-49043600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:49029400-49043600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr3:49029400-49043600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:49029400-49043600	Weak transcription	NH-A	brain
12	chr3:49029400-49043800	Weak transcription	Psoas Muscle	Psoas
13	chr3:49029400-49043800	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr3:49029600-49042000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:49029600-49042200	Weak transcription	Ovary	ovary
16	chr3:49029600-49042400	Weak transcription	HMEC	breast
17	chr3:49029600-49043400	Weak transcription	Esophagus	oesophagus
18	chr3:49029600-49043400	Weak transcription	Fetal Kidney	kidney
19	chr3:49029600-49043400	Weak transcription	GM12878-XiMat	blood
20	chr3:49029600-49043400	Weak transcription	NHDF-Ad	bronchial
21	chr3:49029600-49043600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:49029600-49043600	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:49029600-49043600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:49029600-49043800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr3:49029600-49043800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr3:49029600-49043800	Weak transcription	HSMM	muscle
27	chr3:49029600-49043800	Weak transcription	HSMMtube	muscle
28	chr3:49029800-49043400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr3:49029800-49043400	Weak transcription	Dnd41	blood
30	chr3:49029800-49043600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:49029800-49043600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:49029800-49043600	Weak transcription	A549	lung
33	chr3:49030000-49043400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:49030000-49043800	Weak transcription	Small Intestine	intestine
35	chr3:49031400-49040600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr3:49031600-49043600	Weak transcription	HUVEC	blood vessel
37	chr3:49032000-49043600	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr3:49032200-49041400	Weak transcription	Aorta	Aorta
39	chr3:49032200-49043600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:49032800-49043600	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr3:49033000-49043600	Weak transcription	Osteobl	bone
42	chr3:49033600-49043400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr3:49034800-49043400	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr3:49034800-49043600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:49035000-49041200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr3:49035000-49041800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:49035000-49042200	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr3:49035000-49042200	Weak transcription	NHLF	lung
49	chr3:49035000-49043600	Weak transcription	Primary B cells from peripheral blood	blood
50	chr3:49035000-49043600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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