Variant report

Variant	rs2406690
Chromosome Location	chr13:48489658-48489659
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48480107..48482697-chr13:48488766..48491546,2	K562	blood:

Variant related genes	Relation type
ENSG00000234689	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1408618	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2038789	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4369555	0.83[CHB][hapmap]
rs4508328	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4558305	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4941616	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4942712	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs4942713	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4942715	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7321745	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7330169	0.85[ASN][1000 genomes]
rs7337764	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7981303	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7998090	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9526407	0.87[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs9526410	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9526416	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9534856	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs9534857	0.87[CHB][hapmap]
rs9534859	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9534862	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9534864	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9534867	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9534888	0.81[CHB][hapmap]
rs9562775	0.94[EUR][1000 genomes]
rs9591123	0.92[ASN][1000 genomes]
rs9595815	0.81[YRI][hapmap]

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	esv3510679	chr13:48236624-48498185	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv3510680	chr13:48236624-48498185	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv933980	chr13:48431000-48557419	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv1803690	chr13:48470681-48508091	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2406690	SERP2	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48472200-48491400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr13:48477000-48506400	Weak transcription	Psoas Muscle	Psoas
3	chr13:48478600-48490000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr13:48478800-48491000	Weak transcription	Adipose Nuclei	Adipose
5	chr13:48478800-48491800	Weak transcription	Left Ventricle	heart
6	chr13:48478800-48492200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr13:48481000-48493000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr13:48482800-48494400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr13:48486200-48492000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr13:48488000-48491000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr13:48489400-48492800	Weak transcription	Liver	Liver
12	chr13:48489600-48490200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links