Variant report

Variant	rs7678773
Chromosome Location	chr4:31044237-31044238
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10005651	0.91[ASN][1000 genomes]
rs10033574	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10084945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10939328	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1463851	1.00[YRI][hapmap]
rs1979815	0.89[ASN][1000 genomes]
rs1979816	0.95[ASN][1000 genomes]
rs1979818	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2036245	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28452425	0.89[ASN][1000 genomes]
rs28532843	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28861207	0.91[ASN][1000 genomes]
rs3947332	0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4352437	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4524343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4577529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4615136	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4621393	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4692111	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61441733	0.95[ASN][1000 genomes]
rs6448736	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6448737	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6448738	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6448740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6811512	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6813325	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6820873	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6821627	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6824760	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6828539	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6836089	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6836516	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6838664	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6843199	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6843328	0.91[AMR][1000 genomes]
rs6844794	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6848676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6852025	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7657737	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9990809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998450	chr4:30823631-31628179	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7678773	RFPL1	trans	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:31042000-31045400	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr4:31042600-31045600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:31043200-31050600	Weak transcription	Psoas Muscle	Psoas
4	chr4:31043400-31045600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:31043800-31044400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:31043800-31044600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:31043800-31044800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr4:31043800-31045200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:31043800-31050000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:31043800-31052800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:31044000-31044400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr4:31044000-31044400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr4:31044000-31044400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr4:31044000-31045000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr4:31044000-31046400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:31044200-31045800	Weak transcription	Fetal Heart	heart

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