Variant report

Variant	rs4540944
Chromosome Location	chr13:96182125-96182126
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11619109	0.90[ASN][1000 genomes]
rs2209534	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2389354	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2389355	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4506761	0.85[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.92[LWK][hapmap];0.83[MKK][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7981330	0.85[CHB][hapmap];0.83[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7982853	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7995308	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9302077	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9302078	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9302079	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9516597	0.85[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.92[LWK][hapmap];0.82[MKK][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9524996	0.85[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs9556484	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9556485	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9556486	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9561884	0.88[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9561893	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9561895	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9590295	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9590296	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9590297	0.90[ASN][1000 genomes]
rs9590298	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs971303	0.82[YRI][hapmap];0.87[ASN][1000 genomes]
rs980094	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv525760	chr13:96176034-96186575	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4540944	SPATS1	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96176200-96182400	Weak transcription	Pancreas	Pancrea
2	chr13:96177000-96182200	Weak transcription	Hela-S3	cervix
3	chr13:96177000-96182200	Weak transcription	HMEC	breast
4	chr13:96177000-96182400	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr13:96181200-96185800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr13:96181600-96183000	Enhancers	Primary hematopoietic stem cells	blood
7	chr13:96181600-96183000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr13:96181800-96183000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr13:96181800-96183000	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr13:96181800-96183000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr13:96181800-96183200	Enhancers	HUVEC	blood vessel
12	chr13:96182000-96182400	Bivalent Enhancer	Osteobl	bone
13	chr13:96182000-96182600	Enhancers	NH-A	brain

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