Variant report

Variant	rs695625
Chromosome Location	chr22:28814890-28814891
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1125250	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]
rs1303845	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs134179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs134180	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs134183	0.95[CEU][hapmap]
rs134196	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs134489	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs134500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs134507	1.00[CEU][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs134526	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs134541	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs134543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs134548	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs134551	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17503350	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs2346397	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.95[ASN][1000 genomes]
rs2346867	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34593692	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5752743	0.85[JPT][hapmap]
rs5762629	0.83[CEU][hapmap];0.85[AMR][1000 genomes]
rs5762660	0.85[JPT][hapmap]
rs5762680	0.83[CEU][hapmap]
rs695272	0.96[ASN][1000 genomes]
rs695439	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs695591	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs695659	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs695762	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs695796	0.93[ASN][1000 genomes]
rs695797	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs695625	TTC7B	trans	parietal	SCAN
rs695625	TTC28	cis	lymphoblastoid	seeQTL
rs695625	TTC28	cis	cerebellum	SCAN
rs695625	SEC14L4	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28793000-28819800	Weak transcription	Fetal Intestine Small	intestine
2	chr22:28798800-28821200	Weak transcription	Dnd41	blood
3	chr22:28806800-28815400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr22:28806800-28815800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr22:28807400-28821200	Weak transcription	Hela-S3	cervix
6	chr22:28808400-28821400	Weak transcription	Gastric	stomach
7	chr22:28808400-28821800	Weak transcription	Psoas Muscle	Psoas
8	chr22:28810600-28815000	Weak transcription	HepG2	liver
9	chr22:28810600-28815200	Weak transcription	Fetal Lung	lung
10	chr22:28810600-28816000	Weak transcription	Ovary	ovary
11	chr22:28810600-28821800	Weak transcription	Adipose Nuclei	Adipose
12	chr22:28811000-28821600	Weak transcription	Pancreas	Pancrea
13	chr22:28811800-28815600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr22:28813400-28815800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr22:28813600-28815000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr22:28813600-28816400	Enhancers	Fetal Brain Female	brain
17	chr22:28814000-28817400	Enhancers	Brain Germinal Matrix	brain
18	chr22:28814200-28818000	Enhancers	Fetal Brain Male	brain
19	chr22:28814800-28815200	Enhancers	Rectal Smooth Muscle	rectum
20	chr22:28814800-28815600	Enhancers	Liver	Liver

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