Variant report

Variant	rs4771920
Chromosome Location	chr13:96200552-96200553
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr13:96199564-96200596	SK-N-SH	brain:	n/a	chr13:96200208-96200217 chr13:96200007-96200017
2	GATA3	chr13:96199526-96200651	SK-N-SH	brain:	n/a	chr13:96200208-96200217 chr13:96200007-96200017
3	JUND	chr13:96200523-96200565	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
CLDN10	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1000601	0.92[CEU][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs1952107	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4771921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4773919	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs59483123	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72651928	0.87[EUR][1000 genomes]
rs7995795	0.92[CEU][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs8001332	0.88[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs9516600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9516601	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9516602	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9525011	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9525016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9525017	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9525018	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9525019	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9525020	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9525025	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9525026	0.88[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.85[LWK][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs9525028	0.92[CEU][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs9525029	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs9525030	0.87[EUR][1000 genomes]
rs9525032	0.88[CEU][hapmap];0.88[EUR][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	nsv900933	chr13:96138087-96215289	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4771920	FARP1	cis	cerebellum	SCAN
rs4771920	CLDN10	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96194600-96204200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr13:96194600-96204200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr13:96198800-96200600	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr13:96199000-96200600	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr13:96199000-96200600	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr13:96199400-96201200	Enhancers	H1 Cell Line	embryonic stem cell
7	chr13:96199600-96200600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr13:96199600-96201000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr13:96200200-96200800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr13:96200400-96200600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr13:96200400-96204800	Weak transcription	A549	lung

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