Variant report

Variant	rs2147692
Chromosome Location	chr13:53287023-53287024
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1057478	1.00[ASW][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap]
rs11616261	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11617331	0.85[ASN][1000 genomes]
rs2038826	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2147676	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2575960	1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs342768	0.84[ASN][1000 genomes]
rs342770	0.84[ASN][1000 genomes]
rs3742297	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4284531	0.85[CHB][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap]
rs4301905	0.81[ASN][1000 genomes]
rs4335671	0.81[ASN][1000 genomes]
rs4884235	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4885325	0.85[ASN][1000 genomes]
rs616969	0.82[ASN][1000 genomes]
rs61958118	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6561671	0.86[ASN][1000 genomes]
rs6561675	0.86[ASN][1000 genomes]
rs7139495	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7139630	1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs7324427	0.89[ASN][1000 genomes]
rs7328729	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs7334137	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7334677	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7336771	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7337021	0.88[ASN][1000 genomes]
rs7399901	0.85[ASN][1000 genomes]
rs7997186	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7999849	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9526951	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9526968	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9526974	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9526975	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9526982	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9536197	0.86[ASN][1000 genomes]
rs9536202	0.87[ASN][1000 genomes]
rs9536211	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9536212	0.92[CHB][hapmap];0.87[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9536217	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9536219	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9536220	0.83[CHB][hapmap];0.90[YRI][hapmap]
rs9536223	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9536236	0.95[ASN][1000 genomes]
rs9536247	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9536262	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9563113	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs9563114	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs9568750	0.87[ASN][1000 genomes]
rs9568751	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1044949	chr13:53071140-53289426	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1044051	chr13:53139132-53287023	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv1038942	chr13:53139132-53289426	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1039911	chr13:53139132-53303074	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1037189	chr13:53173013-53287060	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv541775	chr13:53173013-53287060	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1047265	chr13:53173013-53311419	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
10	nsv541776	chr13:53173013-53311419	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2147692	HNRNPA1L2	cis	cerebellum	SCAN
rs2147692	CKAP2	cis	parietal	SCAN
rs2147692	CKAP2	cis	cerebellum	SCAN
rs2147692	CKAP2	cis	multi-tissue	Pritchard
rs2147692	CKAP2	cis	Artery Tibial	GTEx
rs2147692	SUGT1	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53256600-53297800	Weak transcription	Pancreas	Pancrea
2	chr13:53260800-53297000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr13:53272400-53297400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr13:53280400-53287400	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr13:53280600-53294600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr13:53283400-53294600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr13:53285200-53287400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr13:53285200-53287400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr13:53285400-53287200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr13:53285400-53288400	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr13:53285600-53291000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr13:53286200-53287400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr13:53286200-53287800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr13:53286400-53287400	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr13:53286800-53287200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
16	chr13:53286800-53288000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr13:53286800-53288600	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr13:53286800-53310800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr13:53287000-53288000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr13:53287000-53289400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr13:53287000-53294600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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