Variant report

Variant	rs6836118
Chromosome Location	chr4:57370915-57370916
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	chr4:57370557-57372975	K562	blood:	n/a	n/a
2	POLR2A	chr4:57370798-57371020	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ARL9	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10434444	1.00[CEU][hapmap]
rs1060472	0.89[TSI][hapmap]
rs11133442	0.89[TSI][hapmap]
rs11133443	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12498340	1.00[CEU][hapmap];0.89[TSI][hapmap]
rs12501502	0.80[TSI][hapmap]
rs12645138	0.84[ASN][1000 genomes]
rs1520026	0.80[TSI][hapmap]
rs17086696	1.00[CEU][hapmap];0.89[TSI][hapmap]
rs1967559	0.83[TSI][hapmap]
rs1983378	1.00[CEU][hapmap]
rs2271923	0.80[TSI][hapmap]
rs2271925	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34510373	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3796548	1.00[CEU][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3822001	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4493603	0.80[TSI][hapmap]
rs4565139	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4864579	1.00[CEU][hapmap]
rs4865092	1.00[CEU][hapmap]
rs56066795	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56356367	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56672277	0.84[ASN][1000 genomes]
rs60104031	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6554344	0.92[CEU][hapmap]
rs67343558	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67721941	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6853418	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73167398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73240555	0.81[AMR][1000 genomes]
rs7664841	0.89[TSI][hapmap]
rs7696808	1.00[CEU][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.84[ASN][1000 genomes]
rs8340	1.00[CEU][hapmap];0.89[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv829941	chr4:57359551-57553136	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6836118	SRP72	Cis_1M	lymphoblastoid	RTeQTL
rs6836118	AASDH	cis	parietal	SCAN
rs6836118	AASDH	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57334800-57371200	Weak transcription	Stomach Mucosa	stomach
2	chr4:57335200-57371400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:57336000-57371000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:57342400-57371400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:57346000-57371400	Weak transcription	Pancreas	Pancrea
6	chr4:57352000-57371400	Weak transcription	Gastric	stomach
7	chr4:57352000-57371400	Weak transcription	Spleen	Spleen
8	chr4:57353800-57371400	Weak transcription	Fetal Brain Male	brain
9	chr4:57354600-57371400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:57356600-57371400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:57357400-57371400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr4:57357400-57371800	Weak transcription	Small Intestine	intestine
13	chr4:57357600-57371400	Weak transcription	Brain Substantia Nigra	brain
14	chr4:57357800-57371200	Weak transcription	Colonic Mucosa	Colon
15	chr4:57359200-57371200	Weak transcription	Hela-S3	cervix
16	chr4:57360400-57371200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr4:57361200-57371400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:57362400-57371400	Weak transcription	Aorta	Aorta
19	chr4:57362400-57371400	Weak transcription	Esophagus	oesophagus
20	chr4:57362400-57371400	Weak transcription	Right Ventricle	heart
21	chr4:57362600-57371400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:57362600-57371400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr4:57362800-57371400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr4:57363000-57371400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr4:57363000-57371400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:57363200-57371200	Weak transcription	Fetal Stomach	stomach
27	chr4:57363200-57371400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr4:57363200-57371400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:57363200-57371400	Weak transcription	Fetal Lung	lung
30	chr4:57363200-57371400	Weak transcription	Ovary	ovary
31	chr4:57363200-57371400	Weak transcription	NHLF	lung
32	chr4:57363200-57371600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:57363200-57371600	Weak transcription	Lung	lung
34	chr4:57363800-57371400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr4:57363800-57371600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:57364000-57371200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr4:57364000-57371400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr4:57364000-57371400	Weak transcription	Brain Angular Gyrus	brain
39	chr4:57364200-57371400	Weak transcription	Brain Germinal Matrix	brain
40	chr4:57366800-57371400	Weak transcription	Fetal Heart	heart
41	chr4:57367000-57371600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:57367800-57371400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr4:57367800-57371400	Weak transcription	HUVEC	blood vessel
44	chr4:57368000-57371000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr4:57368000-57371200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:57368000-57371400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr4:57368000-57371400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr4:57368000-57371400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr4:57368000-57371400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr4:57368000-57371400	Weak transcription	Fetal Intestine Small	intestine

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