Variant report

Variant	rs2413181
Chromosome Location	chr22:33774359-33774360
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1033373	1.00[ASN][1000 genomes]
rs1033375	1.00[ASN][1000 genomes]
rs11089623	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11705582	0.95[ASN][1000 genomes]
rs12484626	0.89[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13347210	1.00[ASN][1000 genomes]
rs16992213	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16992256	0.93[CEU][hapmap];0.83[CHB][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1807700	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2009700	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2179057	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267195	0.92[CHB][hapmap]
rs2267199	0.83[CHB][hapmap]
rs2283898	0.93[CEU][hapmap];0.83[CHB][hapmap];0.96[EUR][1000 genomes]
rs2283899	0.83[ASW][hapmap];0.93[CEU][hapmap];0.83[CHB][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2283901	0.93[CEU][hapmap];0.83[CHB][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2283902	0.93[CEU][hapmap];0.83[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2283904	0.87[MEX][hapmap]
rs2413182	0.83[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];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998905	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[ASN][1000 genomes]
rs5998906	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5998917	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60262384	1.00[ASN][1000 genomes]
rs60435865	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62225265	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs715487	0.83[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7285067	0.83[ASW][hapmap];0.93[CEU][hapmap];0.83[CHB][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7285513	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7290813	0.93[CEU][hapmap];0.83[CHB][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs7291480	0.83[CHB][hapmap]
rs742008	0.93[CEU][hapmap];0.83[CHB][hapmap]
rs8142296	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9607037	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];1.00[ASN][1000 genomes]
rs9607038	0.92[CHB][hapmap]
rs9607040	1.00[ASN][1000 genomes]
rs9609772	0.91[CHB][hapmap]
rs9609775	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs9609776	1.00[ASN][1000 genomes]
rs9609778	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9609779	0.93[CEU][hapmap];0.83[CHB][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531587	chr22:33346710-33809338	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv948523	chr22:33414164-34098417	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1067068	chr22:33452180-33851033	Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
4	nsv933455	chr22:33532697-33915429	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1059927	chr22:33615699-33904339	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv544682	chr22:33615699-33904339	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1061485	chr22:33670971-33885169	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
8	nsv934109	chr22:33722066-34339500	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
9	nsv459876	chr22:33746624-33776430	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv588898	chr22:33746624-33776430	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1062127	chr22:33755479-34085278	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
12	nsv544683	chr22:33755479-34085278	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
13	esv1835065	chr22:33758698-33798116	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv526030	chr22:33760604-33776430	Weak transcription ZNF genes & repeats Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv1064026	chr22:33767185-33902059	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2413181	RHBDD3	cis	parietal	SCAN
rs2413181	SF3B2	trans	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33731400-33779800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr22:33734000-33777800	Weak transcription	Pancreas	Pancrea
3	chr22:33738000-33776800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr22:33747400-33775600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr22:33757800-33777000	Weak transcription	Fetal Stomach	stomach
6	chr22:33757800-33777200	Weak transcription	Left Ventricle	heart
7	chr22:33765800-33777800	Weak transcription	Gastric	stomach
8	chr22:33766800-33786000	Weak transcription	Fetal Lung	lung
9	chr22:33769200-33777800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr22:33769800-33776400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr22:33770200-33774800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr22:33771800-33776400	Weak transcription	HSMM	muscle
13	chr22:33773000-33778600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr22:33773200-33777200	Weak transcription	Fetal Intestine Large	intestine
15	chr22:33773400-33774600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr22:33773400-33776400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr22:33773600-33774800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
18	chr22:33773600-33775600	Weak transcription	Liver	Liver
19	chr22:33773600-33776200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
20	chr22:33773600-33781200	Weak transcription	Primary B cells from cord blood	blood
21	chr22:33773800-33776200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
22	chr22:33774000-33774800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr22:33774000-33777000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr22:33774000-33777200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr22:33774200-33775000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
26	chr22:33774200-33786200	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links