Variant report

Variant	rs9506244
Chromosome Location	chr13:30518421-30518422
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11841228	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1359475	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4318068	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4769779	0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4769780	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4769781	0.85[CEU][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs512583	0.86[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs566495	0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs576712	0.80[ASN][1000 genomes]
rs634413	0.89[CEU][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs646917	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6490436	0.82[ASN][1000 genomes]
rs6490437	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7322038	0.87[LWK][hapmap];0.87[MEX][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7332851	0.83[ASN][1000 genomes]
rs7334559	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7334714	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7339208	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7994222	0.82[ASW][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs912788	0.83[CEU][hapmap]
rs9314990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9314991	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9314992	0.86[EUR][1000 genomes]
rs9508594	0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv510598	chr13:30476386-30542798	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9506244	FLT1	cis	parietal	SCAN
rs9506244	SH3BGRL2	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30510800-30521600	Weak transcription	Pancreas	Pancrea
2	chr13:30514000-30522600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr13:30516400-30518600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr13:30516400-30518800	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr13:30516600-30518600	Enhancers	H1 Cell Line	embryonic stem cell
6	chr13:30516600-30518600	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr13:30516600-30518800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr13:30516600-30519000	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr13:30516800-30518600	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr13:30517000-30518600	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr13:30517400-30526000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr13:30518000-30518600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr13:30518200-30520000	Weak transcription	Stomach Mucosa	stomach
14	chr13:30518200-30520200	Enhancers	Placenta	Placenta
15	chr13:30518200-30522000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr13:30518400-30520200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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