Variant report

Variant	rs2283899
Chromosome Location	chr22:33798202-33798203
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12484626	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16992213	0.83[CHB][hapmap]
rs16992256	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1807700	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2009700	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179057	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2267196	0.87[ASN][1000 genomes]
rs2267199	0.83[CHB][hapmap]
rs2283898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283904	0.82[CHD][hapmap];0.84[MEX][hapmap]
rs2413180	0.81[JPT][hapmap]
rs2413181	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]
rs2413182	0.93[CEU][hapmap];0.83[CHB][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs5998903	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs5998904	0.89[ASN][1000 genomes]
rs5998905	0.88[MEX][hapmap]
rs5998906	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5998917	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5998933	0.81[ASN][1000 genomes]
rs62225265	0.97[EUR][1000 genomes]
rs715487	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7284548	0.84[ASN][1000 genomes]
rs7285067	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7285513	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7290813	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7291480	0.83[CHB][hapmap]
rs742008	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap]
rs8142296	0.83[CHB][hapmap]
rs9609775	0.83[CHB][hapmap]
rs9609778	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9609779	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9619345	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
10	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
11	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
12	nsv531588	chr22:33776857-34150188	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
13	nsv1058261	chr22:33793423-33823308	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2283899	RHBDD3	cis	parietal	SCAN
rs2283899	SF3B2	trans	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33775600-33800400	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr22:33778200-33800800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr22:33778600-33801000	Weak transcription	GM12878-XiMat	blood
4	chr22:33778600-33852000	Weak transcription	Pancreas	Pancrea
5	chr22:33778800-33800400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr22:33779000-33800000	Weak transcription	Fetal Intestine Small	intestine
7	chr22:33780000-33818000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr22:33780200-33802800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr22:33780600-33805200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr22:33780600-33834000	Weak transcription	Gastric	stomach
11	chr22:33780800-33823000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr22:33781200-33814800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr22:33789800-33800400	Weak transcription	Psoas Muscle	Psoas
14	chr22:33790200-33800400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr22:33790600-33798600	Weak transcription	Liver	Liver
16	chr22:33791400-33801000	Weak transcription	HSMM	muscle
17	chr22:33792800-33811000	Weak transcription	Aorta	Aorta
18	chr22:33795000-33801000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr22:33797000-33814800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr22:33797000-33817800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr22:33797200-33800400	Weak transcription	Right Ventricle	heart
22	chr22:33797400-33800000	Weak transcription	Fetal Heart	heart
23	chr22:33797400-33806800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr22:33797400-33810600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr22:33797400-33818200	Weak transcription	Fetal Stomach	stomach
26	chr22:33797800-33800800	Weak transcription	HSMMtube	muscle
27	chr22:33797800-33802400	Enhancers	HepG2	liver
28	chr22:33797800-33817800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr22:33798000-33800200	Weak transcription	Left Ventricle	heart
30	chr22:33798000-33822800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr22:33798200-33798600	Strong transcription	Ovary	ovary
32	chr22:33798200-33823400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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