Variant report

Variant	rs836235
Chromosome Location	chr2:231402229-231402230
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:48)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:48 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr2:231402056-231402629	GM12878	blood:	n/a	n/a
2	RUNX3	chr2:231401600-231402832	GM12878	blood:	n/a	n/a
3	NFYB	chr2:231402164-231402677	GM12878	blood:	n/a	n/a
4	STAT5A	chr2:231401923-231402645	GM12878	blood:	n/a	n/a
5	BCL11A	chr2:231402173-231402516	GM12878	blood:	n/a	n/a
6	ZNF143	chr2:231402184-231402627	GM12878	blood:	n/a	n/a
7	BHLHE40	chr2:231402165-231402596	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:231402129-231402645	GM12891	blood:	n/a	n/a
9	CEBPB	chr2:231402222-231402483	GM12878	blood:	n/a	n/a
10	EP300	chr2:231402033-231402623	GM12878	blood:	n/a	n/a
11	POLR2A	chr2:231402081-231402832	GM12892	blood:	n/a	n/a
12	EBF1	chr2:231402101-231403455	GM12878	blood:	n/a	chr2:231402870-231402881 chr2:231402846-231402857
13	RCOR1	chr2:231402172-231403030	GM12878	blood:	n/a	n/a
14	MTA3	chr2:231401999-231402804	GM12878	blood:	n/a	n/a
15	SP1	chr2:231402178-231402531	GM12878	blood:	n/a	n/a
16	EP300	chr2:231402178-231402749	GM12878	blood:	n/a	n/a
17	NFIC	chr2:231402032-231402723	GM12878	blood:	n/a	n/a
18	FOXM1	chr2:231401979-231402650	GM12878	blood:	n/a	n/a
19	TBL1XR1	chr2:231402192-231402629	GM12878	blood:	n/a	n/a
20	CTCF	chr2:231402080-231402230	GM12872	blood:	n/a	n/a
21	SMC3	chr2:231402132-231402868	GM12878	blood:	n/a	n/a
22	RELA	chr2:231401983-231402737	GM18505	blood:	n/a	n/a
23	RELA	chr2:231402165-231402582	GM19099	blood:	n/a	n/a
24	NFATC1	chr2:231401863-231402646	GM12878	blood:	n/a	n/a
25	ATF2	chr2:231402096-231402626	GM12878	blood:	n/a	n/a
26	RELA	chr2:231402202-231402687	GM18951	blood:	n/a	n/a
27	PAX5	chr2:231402175-231402620	GM12878	blood:	n/a	n/a
28	RELA	chr2:231402040-231402653	GM10847	blood:	n/a	n/a
29	PML	chr2:231401795-231402955	GM12878	blood:	n/a	n/a
30	WRNIP1	chr2:231402076-231402692	GM12878	blood:	n/a	n/a
31	BCL3	chr2:231402165-231402627	GM12878	blood:	n/a	n/a
32	FOXM1	chr2:231401613-231402784	GM12878	blood:	n/a	n/a
33	STAT5A	chr2:231402028-231402600	GM12878	blood:	n/a	n/a
34	BCLAF1	chr2:231402056-231402744	GM12878	blood:	n/a	n/a
35	BATF	chr2:231402155-231402492	GM12878	blood:	n/a	n/a
36	PAX5	chr2:231402185-231402571	GM12878	blood:	n/a	n/a
37	BCL11A	chr2:231402139-231402620	GM12878	blood:	n/a	n/a
38	PAX5	chr2:231402143-231402656	GM12878	blood:	n/a	n/a
39	CHD2	chr2:231402083-231402624	GM12878	blood:	n/a	n/a
40	STAT3	chr2:231402151-231402549	GM12878	blood:	n/a	n/a
41	NFIC	chr2:231401859-231402749	GM12878	blood:	n/a	n/a
42	NFATC1	chr2:231401862-231402723	GM12878	blood:	n/a	n/a
43	BATF	chr2:231402126-231402585	GM12878	blood:	n/a	n/a
44	RUNX3	chr2:231401136-231403243	GM12878	blood:	n/a	n/a
45	MTA3	chr2:231401568-231403552	GM12878	blood:	n/a	n/a
46	TCF12	chr2:231402218-231402526	GM12878	blood:	n/a	n/a
47	CEBPB	chr2:231402051-231402801	GM12878	blood:	n/a	n/a
48	RELA	chr2:231401622-231402730	GM12891	blood:	n/a	n/a

No data

Variant related genes	Relation type
SP100	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11687978	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1615764	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1649893	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1649895	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1649923	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1678152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1678157	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1678158	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1678175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678184	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678186	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1678188	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1678196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1678197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1678208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2559092	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4972956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4973329	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55736462	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62193429	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62193432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6711920	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6712053	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6740413	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs699662	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs699663	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs836230	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs836231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs836233	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs836234	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs856838	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs866270	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv875948	chr2:231380697-231420401	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv584673	chr2:231385231-231433237	Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs836235	UGT1A1	cis	cerebellum	SCAN
rs836235	TIGD1	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231371000-231409800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr2:231390600-231403800	Weak transcription	Ovary	ovary
3	chr2:231390600-231404000	Weak transcription	Left Ventricle	heart
4	chr2:231390600-231404000	Weak transcription	Lung	lung
5	chr2:231390600-231408200	Weak transcription	Esophagus	oesophagus
6	chr2:231390800-231405600	Weak transcription	Thymus	Thymus
7	chr2:231390800-231409200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:231391000-231406400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:231398000-231405600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:231398400-231406200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr2:231398600-231404000	Weak transcription	Aorta	Aorta
12	chr2:231399000-231404200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr2:231399600-231405000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:231399800-231404000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:231400200-231404600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:231400800-231403200	Enhancers	Primary B cells from peripheral blood	blood
17	chr2:231401000-231404000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr2:231401000-231430200	Weak transcription	Pancreas	Pancrea
19	chr2:231401400-231402800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:231401400-231402800	Flanking Active TSS	GM12878-XiMat	blood
21	chr2:231401400-231405200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr2:231401400-231408600	Weak transcription	Colon Smooth Muscle	Colon
23	chr2:231401600-231403000	Enhancers	Primary B cells from cord blood	blood
24	chr2:231401800-231404000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:231401800-231404000	Weak transcription	Spleen	Spleen
26	chr2:231401800-231404400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:231401800-231406400	Weak transcription	Osteobl	bone
28	chr2:231401800-231409200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr2:231402000-231403800	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr2:231402000-231403800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr2:231402000-231404200	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr2:231402200-231402400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:231402200-231402400	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr2:231402200-231402800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:231402200-231404000	Weak transcription	Primary T cells from cord blood	blood
36	chr2:231402200-231404000	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr2:231402200-231406200	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links