Variant report

Variant	rs4575149
Chromosome Location	chr1:217002691-217002692
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1030846	0.84[CEU][hapmap];0.87[CHB][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap]
rs1126022	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1339337	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1339338	0.84[CEU][hapmap]
rs1339348	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1339356	0.88[CEU][hapmap];0.87[CHB][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap]
rs1344873	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1436888	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1832532	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2032028	0.88[CEU][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes]
rs2118151	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2576234	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2576235	0.83[CEU][hapmap]
rs2576236	0.88[CEU][hapmap]
rs2576238	0.96[CEU][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2789716	0.84[CEU][hapmap];0.87[CHB][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap]
rs2789720	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2813671	0.92[EUR][1000 genomes]
rs2813674	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6604647	0.84[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7512365	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7554036	0.87[CEU][hapmap];0.90[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762163	chr1:216982140-217015625	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4575149	MT3	trans	parietal	SCAN
rs4575149	C1orf97	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216989000-217005800	Weak transcription	Left Ventricle	heart
2	chr1:216994600-217004000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr1:216996400-217004400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr1:216998600-217004000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:216999200-217003800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:216999200-217003800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:216999400-217003200	Weak transcription	Fetal Heart	heart
8	chr1:217000400-217003600	Weak transcription	Fetal Intestine Small	intestine
9	chr1:217001400-217003600	Weak transcription	Fetal Intestine Large	intestine

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