Variant report

Variant	rs10002028
Chromosome Location	chr4:186796912-186796913
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10001944	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13112022	0.83[JPT][hapmap]
rs2603722	0.85[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.89[LWK][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2603724	0.89[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2648107	0.94[CHB][hapmap];0.93[ASN][1000 genomes]
rs2648111	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2648117	0.89[JPT][hapmap]
rs4861686	0.89[ASW][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4862579	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4862580	0.84[ASW][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap];0.93[LWK][hapmap];0.93[MKK][hapmap];0.83[YRI][hapmap]
rs6552931	0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6552932	0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6552935	0.82[CHD][hapmap]
rs6833156	0.82[CHD][hapmap]
rs724072	0.82[CHD][hapmap]
rs7674855	0.85[CHB][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7675409	0.85[CHB][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9994907	0.89[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs9995677	0.85[CHB][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.88[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	nsv1028146	chr4:186503899-187338335	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1023917	chr4:186533075-186997806	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537420	chr4:186533075-186997806	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv530178	chr4:186659940-187478310	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv1015236	chr4:186696172-187004074	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1022661	chr4:186789827-187122464	Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv537422	chr4:186789827-187122464	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10002028	CDKN2AIP	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:186789000-186799600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:186791000-186799600	Weak transcription	Left Ventricle	heart
3	chr4:186791000-186799800	Weak transcription	Pancreas	Pancrea
4	chr4:186791800-186802600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:186793000-186801000	Weak transcription	Spleen	Spleen
6	chr4:186794200-186801400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr4:186795400-186797000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr4:186795400-186797000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr4:186795400-186797000	Enhancers	Hela-S3	cervix
10	chr4:186795400-186797200	Enhancers	Osteobl	bone
11	chr4:186795600-186797000	Enhancers	NHDF-Ad	bronchial
12	chr4:186795600-186797400	Enhancers	HUVEC	blood vessel
13	chr4:186795800-186801600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:186796000-186801800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:186796600-186801200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:186796600-186801200	Weak transcription	HSMMtube	muscle
17	chr4:186796800-186797000	Enhancers	A549	lung
18	chr4:186796800-186797400	Enhancers	Fetal Heart	heart
19	chr4:186796800-186801800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr4:186796800-186802000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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