Variant report

Variant	rs9625475
Chromosome Location	chr22:28841839-28841840
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10483151	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12165708	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12165715	0.91[CEU][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes]
rs12165893	0.91[CEU][hapmap];0.85[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[YRI][hapmap]
rs12166129	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12166245	0.91[CEU][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs12166363	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12166475	0.91[CEU][hapmap];0.85[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12167532	0.84[AMR][1000 genomes]
rs12167667	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12168708	0.85[EUR][1000 genomes]
rs12168765	0.90[CEU][hapmap];0.96[YRI][hapmap]
rs12168851	0.81[EUR][1000 genomes]
rs12169120	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12169595	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12169966	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12170637	0.91[CEU][hapmap]
rs1297607	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs134194	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs134197	0.91[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs134488	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs134506	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs134514	0.91[CEU][hapmap];0.88[MEX][hapmap]
rs134524	0.91[CEU][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes]
rs134547	0.91[CEU][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1474961	0.91[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs16986398	0.91[CEU][hapmap];0.85[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs16986509	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17413461	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2013784	0.91[CEU][hapmap];0.96[YRI][hapmap]
rs2144922	0.91[CEU][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.96[YRI][hapmap]
rs55738739	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56391942	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57871917	0.94[AMR][1000 genomes]
rs58542867	0.81[AFR][1000 genomes]
rs59262169	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60042154	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6005807	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60065194	0.81[AFR][1000 genomes]
rs6519753	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7289534	0.91[CEU][hapmap];0.85[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[YRI][hapmap]
rs7289625	0.91[CEU][hapmap];0.84[AMR][1000 genomes]
rs7291268	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7293232	0.91[CEU][hapmap];0.85[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[YRI][hapmap]
rs73430118	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs73430123	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73430136	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73430155	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73430179	0.81[AFR][1000 genomes]
rs73430186	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73430189	0.81[AMR][1000 genomes]
rs73437900	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73439811	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs738200	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs738627	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8137200	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8137808	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9306457	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9620779	1.00[CEU][hapmap]
rs9620797	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9620799	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9620803	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9620804	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9620808	0.91[CEU][hapmap];0.96[YRI][hapmap]
rs9620809	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9625440	0.91[CEU][hapmap]
rs9625447	0.91[CEU][hapmap]
rs9625467	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9625477	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9625478	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9625481	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9625484	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9625487	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9625492	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9625498	0.81[AFR][1000 genomes]
rs9625501	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9625508	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9625510	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9625512	0.91[CEU][hapmap];0.96[YRI][hapmap]
rs9625513	0.91[CEU][hapmap];0.96[YRI][hapmap]
rs9625514	0.84[CEU][hapmap];0.96[YRI][hapmap]
rs9625515	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9625516	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9625520	0.91[CEU][hapmap];0.85[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[YRI][hapmap]
rs9625521	0.91[CEU][hapmap];0.96[YRI][hapmap]
rs9625522	0.82[AFR][1000 genomes]
rs9625523	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
rs9625475	TTC28	cis	lymphoblastoid	seeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28839600-28844600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr22:28839600-28844600	Weak transcription	K562	blood
3	chr22:28839800-28842200	Weak transcription	Fetal Intestine Large	intestine
4	chr22:28839800-28842400	Weak transcription	Fetal Intestine Small	intestine
5	chr22:28839800-28842400	Weak transcription	Psoas Muscle	Psoas
6	chr22:28839800-28842400	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr22:28839800-28843200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr22:28839800-28843600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr22:28839800-28844200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr22:28839800-28844600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr22:28839800-28844600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr22:28839800-28861200	Weak transcription	Ovary	ovary
13	chr22:28840000-28844600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr22:28840000-28844600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr22:28840000-28844600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr22:28840000-28844600	Weak transcription	Fetal Kidney	kidney
17	chr22:28840000-28844800	Weak transcription	HUVEC	blood vessel
18	chr22:28840000-28845200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr22:28840000-28847000	Weak transcription	Fetal Lung	lung
20	chr22:28840000-28849600	Weak transcription	Fetal Brain Male	brain
21	chr22:28840400-28843000	Weak transcription	Fetal Brain Female	brain
22	chr22:28840400-28844200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr22:28840400-28844600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr22:28841200-28845800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr22:28841600-28842200	Weak transcription	Duodenum Mucosa	Duodenum

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