Variant report

Variant	rs1414041
Chromosome Location	chr10:25853521-25853522
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10082439	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10218998	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1029179	0.86[ASN][1000 genomes]
rs10741094	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10764558	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10764559	0.87[JPT][hapmap]
rs10764562	0.86[JPT][hapmap]
rs10828818	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10828819	0.89[YRI][hapmap]
rs11014610	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11014612	0.87[JPT][hapmap]
rs1335199	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1335200	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1414040	0.87[JPT][hapmap]
rs1414042	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1414043	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1414045	0.87[JPT][hapmap]
rs1414052	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1556665	0.84[ASN][1000 genomes]
rs1855671	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1981117	0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4550137	0.91[ASN][1000 genomes]
rs4747530	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4749046	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4749047	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6482493	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6482494	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7088106	0.87[JPT][hapmap]
rs7090998	0.88[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes]
rs7091908	0.90[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7100209	0.83[JPT][hapmap]
rs7100629	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7101141	0.87[JPT][hapmap]
rs7358105	0.83[JPT][hapmap]
rs7899012	0.89[YRI][hapmap]
rs7901206	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7902319	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7903204	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7903336	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7911256	0.87[JPT][hapmap]
rs7913399	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7915074	0.83[JPT][hapmap]
rs7917704	0.83[JPT][hapmap]
rs7919640	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7922752	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9919420	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[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	esv3349863	chr10:25614571-25946379	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv550227	chr10:25843019-25865744	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv894972	chr10:25849998-25917909	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1414041	PRTFDC1	cis	parietal	SCAN
rs1414041	CATSPERG	trans	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:25847200-25861200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr10:25851000-25854400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr10:25851200-25854400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr10:25851200-25854400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr10:25853400-25853600	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr10:25853400-25853800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr10:25853400-25855400	Enhancers	HUES48 Cell Line	embryonic stem cell

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