Variant report

Variant	rs9852954
Chromosome Location	chr3:132911592-132911593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12695588	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13077843	1.00[JPT][hapmap]
rs13323117	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1450049	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[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]
rs1450050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1450054	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1868602	0.89[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1901039	0.87[TSI][hapmap]
rs28536096	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28539256	0.81[ASN][1000 genomes]
rs28552867	0.95[ASN][1000 genomes]
rs28672850	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4361277	0.81[AMR][1000 genomes]
rs4854701	0.87[TSI][hapmap]
rs4854702	0.87[TSI][hapmap]
rs6781596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792137	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794137	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6809255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71315690	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7618220	1.00[JPT][hapmap];0.87[TSI][hapmap]
rs7628842	0.87[TSI][hapmap]
rs9817924	0.81[ASN][1000 genomes]
rs9820056	0.84[TSI][hapmap]
rs9820287	0.85[ASN][1000 genomes]
rs9837497	0.81[ASN][1000 genomes]
rs9838197	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9848953	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs9852976	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858099	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877365	0.85[ASN][1000 genomes]
rs9877504	0.85[ASN][1000 genomes]
rs9968156	0.87[TSI][hapmap]

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	nsv1000962	chr3:132115062-132919907	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv530055	chr3:132380878-132982343	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9852954	ASTE1	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:132899600-132912000	Enhancers	Fetal Brain Male	brain
2	chr3:132909800-132913600	Weak transcription	Fetal Brain Female	brain
3	chr3:132910200-132912000	Enhancers	Fetal Heart	heart
4	chr3:132910400-132911600	Enhancers	H9 Cell Line	embryonic stem cell
5	chr3:132910400-132911600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr3:132910400-132912000	Enhancers	Fetal Lung	lung
7	chr3:132910600-132911800	Enhancers	Right Atrium	heart
8	chr3:132910600-132911800	Enhancers	HSMMtube	muscle
9	chr3:132910600-132912000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr3:132910800-132911600	Enhancers	Lung	lung
11	chr3:132910800-132911800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:132910800-132912000	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr3:132910800-132912200	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr3:132910800-132912400	Enhancers	NH-A	brain
15	chr3:132911000-132911600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr3:132911000-132911800	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr3:132911000-132912000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:132911200-132911600	Enhancers	Spleen	Spleen
19	chr3:132911200-132912000	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr3:132911400-132911800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:132911400-132911800	Enhancers	Psoas Muscle	Psoas

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