Variant report

Variant	rs9556486
Chromosome Location	chr13:96176681-96176682
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11619109	0.89[ASN][1000 genomes]
rs2209534	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2389354	0.92[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2389355	0.92[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4506761	0.85[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs4540944	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]
rs7981330	0.85[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs7982853	0.88[ASN][1000 genomes]
rs7995308	0.92[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9302077	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9302078	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9302079	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9516597	0.85[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.90[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];0.81[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9556485	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9561884	0.88[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9561893	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9561895	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9590295	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9590296	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9590297	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9590298	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs971303	0.87[ASN][1000 genomes]
rs980094	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]

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	esv2752652	chr13:96059024-96181597	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	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
3	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
rs9556486	SPATS1	trans	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96175800-96177000	Enhancers	Monocytes-CD14+_RO01746	blood
2	chr13:96175800-96177200	Enhancers	NHEK	skin
3	chr13:96176000-96177000	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr13:96176000-96177000	Enhancers	HMEC	breast
5	chr13:96176200-96178000	Weak transcription	Stomach Mucosa	stomach
6	chr13:96176200-96182400	Weak transcription	Pancreas	Pancrea
7	chr13:96176400-96179400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr13:96176600-96177000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr13:96176600-96177000	Enhancers	Hela-S3	cervix
10	chr13:96176600-96181800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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