Variant report

Variant	rs3805184
Chromosome Location	chr4:48138235-48138236
allele	C/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	chr4:48137241-48138609	GM12892	blood:	n/a	n/a
2	POLR2A	chr4:48136964-48138816	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:48137561-48138741	GM12891	blood:	n/a	n/a
4	POLR2A	chr4:48137580-48138539	GM12891	blood:	n/a	n/a
5	POLR2A	chr4:48137788-48138663	GM12892	blood:	n/a	n/a
6	POLR2A	chr4:48137859-48138396	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:48138214-48138483	GM12878	blood:	n/a	n/a
8	POLR2A	chr4:48137622-48138647	GM12892	blood:	n/a	n/a
9	POLR2A	chr4:48137727-48138638	GM12891	blood:	n/a	n/a
10	POLR2A	chr4:48137593-48138531	GM12892	blood:	n/a	n/a
11	POLR2A	chr4:48137778-48141212	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
TXK	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10027991	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10805164	1.00[JPT][hapmap]
rs10805165	1.00[JPT][hapmap]
rs10938524	0.85[ASN][1000 genomes]
rs11730441	0.85[JPT][hapmap]
rs11944549	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11945978	1.00[JPT][hapmap]
rs12332001	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12499541	1.00[JPT][hapmap]
rs12512766	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13104849	1.00[JPT][hapmap]
rs1466994	1.00[JPT][hapmap]
rs1507919	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860999	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1961975	1.00[JPT][hapmap]
rs2089509	1.00[JPT][hapmap]
rs2089510	0.94[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];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2089511	1.00[JPT][hapmap]
rs2243840	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271173	1.00[JPT][hapmap]
rs2464502	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2661529	0.93[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];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2661543	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2661544	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2661547	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]
rs2661548	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]
rs2704399	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2704426	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2704433	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2704435	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2704436	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704439	0.83[GIH][hapmap];0.87[TSI][hapmap]
rs3792620	1.00[JPT][hapmap]
rs3792621	1.00[JPT][hapmap]
rs3792622	1.00[JPT][hapmap]
rs3805179	1.00[JPT][hapmap]
rs4695340	1.00[JPT][hapmap]
rs4695341	0.94[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];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4695344	1.00[JPT][hapmap]
rs6447616	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6819592	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6845941	1.00[JPT][hapmap]
rs7659164	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7678246	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7689953	0.94[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];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs882715	0.88[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
rs3805184	TXK	cis	lymphoblastoid	seeQTL
rs3805184	TXK	cis	multi-tissue	Pritchard
rs3805184	TXK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48129800-48140800	Weak transcription	Fetal Stomach	stomach
2	chr4:48129800-48157400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:48130400-48138400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr4:48130400-48139000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:48130400-48139800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr4:48130400-48152200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr4:48130400-48155400	Weak transcription	Psoas Muscle	Psoas
8	chr4:48130400-48156200	Weak transcription	Adipose Nuclei	Adipose
9	chr4:48130400-48156800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr4:48130400-48157600	Weak transcription	Colonic Mucosa	Colon
11	chr4:48130600-48142800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr4:48130600-48146000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr4:48131800-48141400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:48131800-48142000	Weak transcription	NHLF	lung
15	chr4:48132000-48141400	Weak transcription	HUVEC	blood vessel
16	chr4:48132000-48141600	Weak transcription	NHDF-Ad	bronchial
17	chr4:48132000-48157000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:48132000-48157200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:48132200-48138800	Weak transcription	Stomach Mucosa	stomach
20	chr4:48132200-48139800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr4:48132200-48141800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:48132400-48142000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr4:48132600-48140200	Weak transcription	Right Ventricle	heart
24	chr4:48132600-48141000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:48133000-48141800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr4:48133000-48151400	Weak transcription	HSMMtube	muscle
27	chr4:48133000-48153000	Weak transcription	Placenta	Placenta
28	chr4:48133200-48140400	Weak transcription	Left Ventricle	heart
29	chr4:48133200-48141000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr4:48133200-48141800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr4:48134600-48140600	Weak transcription	Fetal Kidney	kidney
32	chr4:48134800-48141400	Weak transcription	Fetal Brain Male	brain
33	chr4:48135400-48140400	Strong transcription	GM12878-XiMat	blood
34	chr4:48135400-48142200	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr4:48135600-48142800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr4:48136000-48140400	Weak transcription	Small Intestine	intestine
37	chr4:48136000-48140600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr4:48136000-48141000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr4:48136200-48139400	Strong transcription	Primary B cells from peripheral blood	blood
40	chr4:48136400-48139800	Strong transcription	Primary hematopoietic stem cells	blood
41	chr4:48136400-48139800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr4:48136400-48141200	Strong transcription	K562	blood
43	chr4:48136600-48139000	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr4:48136600-48139000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr4:48136600-48139800	Enhancers	Primary T cells fromperipheralblood	blood
46	chr4:48136600-48139800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr4:48136800-48139000	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr4:48136800-48139400	Strong transcription	Primary B cells from cord blood	blood
49	chr4:48136800-48139600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr4:48136800-48139800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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