Variant report

Variant	rs469727
Chromosome Location	chr5:112242968-112242969
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	chr5:112242762-112243286	GM12878	blood:	n/a	n/a
2	POLR2A	chr5:112242826-112243256	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr5:112242829-112243082	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112195332..112197808-chr5:112240725..112243513,2	K562	blood:

Variant related genes	Relation type
ENSG00000266499	TF binding region
ENSG00000272869	Chromatin interaction
ENSG00000153037	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1069061	0.84[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1093611	1.00[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs1093677	0.84[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs149192	0.81[JPT][hapmap]
rs151976	0.87[CEU][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs151977	0.83[ASW][hapmap];0.84[CEU][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs151978	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs153545	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs153546	0.88[CEU][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs153548	1.00[CEU][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs153550	0.85[EUR][1000 genomes]
rs153558	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs153562	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs153565	0.87[EUR][1000 genomes]
rs153571	0.80[MEX][hapmap]
rs173466	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs193527	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2431238	0.84[GIH][hapmap];0.80[MEX][hapmap]
rs2439591	0.87[GIH][hapmap];0.80[MEX][hapmap]
rs2464805	0.87[GIH][hapmap]
rs2545162	0.88[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap]
rs2545165	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs2545166	0.84[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2545167	0.82[ASW][hapmap];0.84[CEU][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2545169	0.87[GIH][hapmap]
rs2909786	0.81[JPT][hapmap]
rs2909787	0.81[JPT][hapmap]
rs2909904	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2909958	0.90[JPT][hapmap]
rs2952615	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs351767	0.81[EUR][1000 genomes]
rs351769	0.88[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs351770	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs351771	0.84[CEU][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap]
rs35726351	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs368575	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs372492	0.84[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs380144	0.86[AMR][1000 genomes]
rs382260	0.84[CEU][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs386830	0.86[ASN][1000 genomes]
rs397768	0.83[ASN][1000 genomes]
rs41115	0.84[CEU][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs411356	0.91[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap]
rs419632	0.88[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs42427	0.84[CEU][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap]
rs429427	0.80[CEU][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs430665	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs431287	0.84[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs433429	0.86[ASN][1000 genomes]
rs434090	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs434157	0.84[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes]
rs438252	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs439456	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs446567	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs455412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs455469	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs456313	0.88[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs458451	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs459102	0.93[EUR][1000 genomes]
rs460301	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs460832	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs461424	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs461866	1.00[CEU][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs463229	0.84[CEU][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs464708	0.88[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap]
rs465454	0.88[CEU][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs465899	0.84[CEU][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs466443	0.82[ASN][1000 genomes]
rs468101	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs468610	0.99[EUR][1000 genomes]
rs468783	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs468854	0.99[EUR][1000 genomes]
rs469663	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs469760	0.88[CEU][hapmap];0.90[JPT][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs469827	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs481789	0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs495794	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs497844	0.92[CEU][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs501250	0.84[CEU][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap]
rs514763	0.83[EUR][1000 genomes]
rs519397	0.88[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs565453	0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs565603	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs580237	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs698405	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712662	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs712663	0.90[EUR][1000 genomes]
rs712664	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs712665	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs712666	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs712668	0.84[CEU][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs712671	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7213	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs818423	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs818424	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs818425	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs818426	0.82[ASN][1000 genomes]
rs818427	0.84[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs818429	0.93[EUR][1000 genomes]
rs818782	0.89[ASN][1000 genomes]
rs864682	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs866006	0.81[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs9011	0.88[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv529536	chr5:112174106-112269758	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv870231	chr5:112192379-112247084	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1030103	chr5:112197662-112255712	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv537863	chr5:112197662-112255712	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1019756	chr5:112242315-112325943	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Attention deficit hyperactivity disorder	18839057	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs469727	TRIM36	cis	cerebellum	SCAN
rs469727	NCRNA00219	cis	parietal	SCAN
rs469727	SRP19	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112211600-112256400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:112212200-112256400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:112212600-112251400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr5:112215200-112255800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr5:112215800-112247200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:112221800-112256600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:112222000-112256400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr5:112223000-112243000	Weak transcription	Right Ventricle	heart
9	chr5:112223000-112245200	Weak transcription	Colonic Mucosa	Colon
10	chr5:112223000-112245200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr5:112223000-112256400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr5:112223000-112256600	Weak transcription	Thymus	Thymus
13	chr5:112224800-112250600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr5:112225000-112251600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr5:112229600-112250000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr5:112229600-112256600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr5:112230200-112251600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr5:112232600-112250200	Weak transcription	Stomach Mucosa	stomach
19	chr5:112233600-112246600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr5:112234200-112249400	Weak transcription	Fetal Heart	heart
21	chr5:112234600-112246400	Weak transcription	HMEC	breast
22	chr5:112235200-112245200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr5:112236400-112245200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr5:112236400-112245600	Weak transcription	Esophagus	oesophagus
25	chr5:112237000-112244600	Weak transcription	NHDF-Ad	bronchial
26	chr5:112237200-112249400	Weak transcription	K562	blood
27	chr5:112237400-112254000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr5:112238200-112245200	Weak transcription	Fetal Thymus	thymus
29	chr5:112238200-112249600	Weak transcription	Brain Germinal Matrix	brain
30	chr5:112238200-112251600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr5:112238400-112244800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr5:112238400-112251800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr5:112238400-112252800	Weak transcription	Small Intestine	intestine
34	chr5:112238400-112253800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr5:112238600-112244800	Weak transcription	NHLF	lung
36	chr5:112238600-112245200	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr5:112238600-112245200	Weak transcription	Colon Smooth Muscle	Colon
38	chr5:112238600-112245400	Weak transcription	A549	lung
39	chr5:112238600-112246400	Weak transcription	Aorta	Aorta
40	chr5:112238600-112248400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:112238800-112244800	Weak transcription	HUVEC	blood vessel
42	chr5:112238800-112245200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr5:112238800-112246200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr5:112239000-112249200	Weak transcription	Hela-S3	cervix
45	chr5:112240600-112243400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr5:112241200-112243400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr5:112241200-112243600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr5:112241200-112244800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:112241200-112247000	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr5:112241200-112250400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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