Variant report

Variant	rs1125250
Chromosome Location	chr22:28984447-28984448
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs134526	0.83[ASN][1000 genomes]
rs134541	0.95[CEU][hapmap];0.89[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs134543	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs134548	0.83[ASW][hapmap];0.95[CEU][hapmap];0.84[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs134551	0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[ASN][1000 genomes]
rs17503350	0.91[CEU][hapmap]
rs1986052	0.94[AMR][1000 genomes]
rs2346397	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.90[ASN][1000 genomes]
rs2346867	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34387654	0.81[EUR][1000 genomes]
rs34593692	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4035540	0.82[ASW][hapmap];0.95[CEU][hapmap];0.89[CHB][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap]
rs5752743	0.85[JPT][hapmap]
rs5762629	0.87[CEU][hapmap]
rs5762660	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs5762680	0.87[CEU][hapmap]
rs5762694	0.87[AMR][1000 genomes]
rs6005835	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs695272	0.91[ASN][1000 genomes]
rs695439	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs695591	0.95[CEU][hapmap];0.89[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs695625	0.94[ASW][hapmap];0.95[CEU][hapmap];0.84[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs695659	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs695762	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs695796	0.88[ASN][1000 genomes]
rs695797	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067544	chr22:28755418-29055246	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv544674	chr22:28755418-29055246	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS 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 miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv588880	chr22:28807277-29001789	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1125250	TTC28	cis	lymphoblastoid	seeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28956800-28993200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr22:28967800-28991600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr22:28967800-28997600	Weak transcription	HepG2	liver
4	chr22:28979200-28991400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr22:28979200-28993600	Weak transcription	Fetal Stomach	stomach
6	chr22:28979600-28990400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr22:28980000-28990600	Weak transcription	Colon Smooth Muscle	Colon
8	chr22:28980400-28990600	Weak transcription	NHLF	lung
9	chr22:28980600-28985600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr22:28981400-28989400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr22:28981600-28990400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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