Variant report

Variant	rs2661547
Chromosome Location	chr4:48147612-48147613
allele	G/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	chr4:48147090-48148107	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
TEC	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10027991	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10805164	1.00[JPT][hapmap]
rs10805165	1.00[JPT][hapmap]
rs10938524	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11730441	0.85[JPT][hapmap]
rs11944549	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11945978	1.00[JPT][hapmap]
rs12332001	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12499541	1.00[JPT][hapmap]
rs12512766	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13104849	1.00[JPT][hapmap]
rs1466994	1.00[JPT][hapmap]
rs1507919	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860999	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1961975	1.00[JPT][hapmap]
rs2089509	1.00[JPT][hapmap]
rs2089510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2089511	1.00[JPT][hapmap]
rs2243840	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271173	1.00[JPT][hapmap]
rs2464502	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2661529	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2661543	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2661544	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2661548	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2704426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704433	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2704435	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2704436	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704439	0.83[GIH][hapmap]
rs3792620	1.00[JPT][hapmap]
rs3792621	1.00[JPT][hapmap]
rs3792622	1.00[JPT][hapmap]
rs3805179	1.00[JPT][hapmap]
rs3805184	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4235153	0.86[YRI][hapmap]
rs4695340	1.00[JPT][hapmap]
rs4695341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4695344	1.00[JPT][hapmap]
rs6447616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814443	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6819592	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6845941	1.00[JPT][hapmap]
rs7659164	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7678246	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7689953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs882715	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2661547	TXK	cis	lymphoblastoid	seeQTL
rs2661547	TXK	cis	multi-tissue	Pritchard
rs2661547	TEC	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48129800-48157400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:48130400-48152200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:48130400-48155400	Weak transcription	Psoas Muscle	Psoas
4	chr4:48130400-48156200	Weak transcription	Adipose Nuclei	Adipose
5	chr4:48130400-48156800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:48130400-48157600	Weak transcription	Colonic Mucosa	Colon
7	chr4:48132000-48157000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:48132000-48157200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:48133000-48151400	Weak transcription	HSMMtube	muscle
10	chr4:48133000-48153000	Weak transcription	Placenta	Placenta
11	chr4:48137800-48153600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:48138400-48157400	Weak transcription	Aorta	Aorta
13	chr4:48138600-48150400	Weak transcription	Fetal Lung	lung
14	chr4:48138600-48155800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:48139200-48154600	Weak transcription	Fetal Intestine Small	intestine
16	chr4:48139200-48155600	Weak transcription	Fetal Intestine Large	intestine
17	chr4:48139200-48157600	Weak transcription	Gastric	stomach
18	chr4:48139200-48159000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:48139800-48155400	Weak transcription	Spleen	Spleen
20	chr4:48139800-48155800	Weak transcription	Lung	lung
21	chr4:48140200-48157400	Weak transcription	Pancreas	Pancrea
22	chr4:48141000-48152200	Weak transcription	Left Ventricle	heart
23	chr4:48141000-48155800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr4:48141200-48151600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr4:48141200-48155400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr4:48141800-48155600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr4:48142400-48155600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:48142600-48155400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr4:48142800-48152200	Strong transcription	GM12878-XiMat	blood
30	chr4:48143000-48148800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr4:48143000-48152200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:48143000-48155800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr4:48143000-48157600	Weak transcription	Fetal Thymus	thymus
34	chr4:48143000-48157600	Weak transcription	Thymus	Thymus
35	chr4:48143200-48155600	Weak transcription	Primary T cells from cord blood	blood
36	chr4:48144000-48155400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:48144400-48151800	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr4:48144400-48155800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr4:48144600-48151600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr4:48144800-48157200	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr4:48145000-48147800	Strong transcription	Primary B cells from peripheral blood	blood
42	chr4:48145600-48147800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr4:48145800-48151400	Weak transcription	K562	blood
44	chr4:48146600-48156000	Strong transcription	Primary hematopoietic stem cells	blood
45	chr4:48146800-48147800	Strong transcription	Duodenum Mucosa	Duodenum
46	chr4:48147000-48148000	Strong transcription	Primary B cells from cord blood	blood
47	chr4:48147600-48150400	Weak transcription	Liver	Liver
48	chr4:48147600-48155600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr4:48147600-48155600	Weak transcription	Esophagus	oesophagus

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