Variant report

Variant	rs9288435
Chromosome Location	chr2:212463224-212463225
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1009142	0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10177211	0.87[EUR][1000 genomes]
rs10177258	0.87[EUR][1000 genomes]
rs10203022	0.89[GIH][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs10210942	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10804199	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10932386	0.88[ASN][1000 genomes]
rs10932387	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs10932388	0.98[EUR][1000 genomes]
rs11679779	0.88[ASN][1000 genomes]
rs11679860	0.88[ASN][1000 genomes]
rs11687988	0.88[ASN][1000 genomes]
rs11691078	0.90[ASN][1000 genomes]
rs11695852	0.84[ASN][1000 genomes]
rs12104775	0.87[EUR][1000 genomes]
rs12465773	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12614500	0.92[ASN][1000 genomes]
rs12619171	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12694243	0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12694245	0.88[ASN][1000 genomes]
rs13007756	0.88[ASN][1000 genomes]
rs1818751	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1829610	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1829611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1851196	1.00[ASW][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1851197	0.87[EUR][1000 genomes]
rs1851198	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1851199	0.87[EUR][1000 genomes]
rs1965462	0.88[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1972142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1972143	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976834	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2371303	0.86[ASN][1000 genomes]
rs2371304	0.84[ASN][1000 genomes]
rs2371305	0.86[ASN][1000 genomes]
rs2888004	0.83[ASN][1000 genomes]
rs4488593	0.81[CEU][hapmap];0.88[ASN][1000 genomes]
rs4599046	0.82[GIH][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs4640322	0.86[ASN][1000 genomes]
rs4672619	0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4673623	0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4673624	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6721804	0.90[ASN][1000 genomes]
rs6731454	0.84[ASN][1000 genomes]
rs7556879	0.93[ASW][hapmap];0.81[CEU][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs7559679	0.90[MEX][hapmap];0.83[TSI][hapmap]
rs7561282	0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7572669	0.90[ASN][1000 genomes]
rs7580963	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7595207	0.86[ASN][1000 genomes]
rs7595223	0.86[ASN][1000 genomes]
rs7602185	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9288434	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9288436	0.92[TSI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000722	chr2:212272622-212465143	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv460069	chr2:212415948-212471642	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv584320	chr2:212415948-212471642	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv584321	chr2:212446818-212511895	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9288435	CPS1IT1	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:212452400-212466800	Weak transcription	Aorta	Aorta
2	chr2:212456600-212473600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:212462600-212465800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:212462800-212464000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:212462800-212464200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:212462800-212465800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:212463000-212464400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr2:212463200-212463600	Weak transcription	Fetal Heart	heart
9	chr2:212463200-212464000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links