Variant report

Variant	rs2485495
Chromosome Location	chr13:38569255-38569256
allele	C/T
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	SRF	chr13:38569155-38569560	ECC-1	luminal epithelium:	n/a	n/a
2	REST	chr13:38568937-38569930	H1-neurons	neurons:	n/a	n/a
3	REST	chr13:38569117-38569657	H1-neurons	neurons:	n/a	n/a
4	MAX	chr13:38569197-38569637	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
HSPD1P9	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12429115	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12853478	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1337594	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1337595	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1337605	0.82[EUR][1000 genomes]
rs1538153	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1538155	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1556781	0.83[EUR][1000 genomes]
rs1591672	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2095673	0.82[AMR][1000 genomes]
rs2250286	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2485286	0.82[EUR][1000 genomes]
rs2485291	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2485298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485483	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2485497	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2485501	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35140422	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36130652	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4270042	0.89[EUR][1000 genomes]
rs67462211	0.84[EUR][1000 genomes]
rs71423167	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73172572	0.89[EUR][1000 genomes]
rs945859	0.82[EUR][1000 genomes]
rs9566279	0.89[EUR][1000 genomes]
rs9566294	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9576402	0.83[EUR][1000 genomes]
rs9576405	0.85[EUR][1000 genomes]
rs9576406	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9576414	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9576424	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9576427	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915901	chr13:38199035-39032633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv899996	chr13:38459224-38577056	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv899998	chr13:38480878-38582178	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv869125	chr13:38550449-39132813	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv949406	chr13:38561474-39033484	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38568400-38570000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:38568400-38570000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr13:38568600-38569800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr13:38568600-38569800	Enhancers	Brain Germinal Matrix	brain
5	chr13:38568800-38569800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr13:38569000-38569800	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr13:38569000-38569800	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr13:38569200-38569600	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr13:38569200-38569600	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr13:38569200-38569600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr13:38569200-38569600	Enhancers	Fetal Brain Male	brain
12	chr13:38569200-38569800	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr13:38569200-38569800	Enhancers	Fetal Kidney	kidney

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