Variant report

Variant	rs8137254
Chromosome Location	chr22:29429997-29429998
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr22:29429860-29430010	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr22:29428793..29430315-chr22:29546051..29548231,2	K562	blood:
2	chr22:29429778..29432047-chr22:29449305..29452097,2	K562	blood:
3	chr22:29429893..29432783-chr22:29435489..29437651,2	K562	blood:
4	chr22:29193926..29196590-chr22:29426887..29431178,4	K562	blood:
5	chr22:29194383..29198112-chr22:29429822..29431931,3	MCF-7	breast:
6	chr22:29427479..29429172-chr22:29429415..29431878,2	K562	blood:
7	chr22:29275977..29281461-chr22:29425203..29430435,9	MCF-7	breast:

No data

Variant related genes	Relation type
ZNRF3-AS1	TF binding region
ENSG00000226471	Chromatin interaction
ENSG00000183579	Chromatin interaction
ENSG00000100219	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs12484832	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs12485244	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs132565	0.82[AMR][1000 genomes]
rs17440734	0.92[CEU][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1883197	0.84[EUR][1000 genomes]
rs1977047	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1983553	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2064084	0.96[CEU][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2072774	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2103544	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2347789	0.82[EUR][1000 genomes]
rs2347790	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28541979	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4140643	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4333023	0.82[EUR][1000 genomes]
rs4404379	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4594553	0.80[ASN][1000 genomes]
rs469994	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs4820794	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4823002	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4823003	0.96[CEU][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes]
rs4823005	0.96[CEU][hapmap];0.85[AMR][1000 genomes]
rs5997430	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5997431	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5997432	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5997433	0.96[CEU][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs5997434	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5997435	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6005954	0.85[AMR][1000 genomes]
rs6005955	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6005956	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6005958	0.96[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6005959	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6005964	0.92[CEU][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6005965	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs6005967	0.96[CEU][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs713834	0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs727892	0.92[CEU][hapmap];0.80[GIH][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs7284304	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7287517	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7290304	0.96[CEU][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes]
rs738246	0.96[CEU][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs8137499	0.92[CEU][hapmap];0.82[AMR][1000 genomes]
rs8142591	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs874915	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs874916	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs874917	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9608719	0.96[CEU][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9608720	0.82[CEU][hapmap]
rs9608721	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9613771	0.83[EUR][1000 genomes]
rs9613776	1.00[CEU][hapmap];0.82[JPT][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9613777	1.00[CEU][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9613780	0.82[CEU][hapmap]
rs9613782	0.82[CEU][hapmap]
rs9613784	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9613785	0.96[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs964589	0.96[CEU][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8137254	GGT5	cis	parietal	SCAN
rs8137254	SEZ6L	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29426400-29430000	Enhancers	Lung	lung
2	chr22:29426800-29430000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr22:29427200-29430200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr22:29427200-29430600	Enhancers	Right Atrium	heart
5	chr22:29427400-29448400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr22:29427800-29430400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr22:29427800-29431200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr22:29427800-29436600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr22:29427800-29451400	Weak transcription	Psoas Muscle	Psoas
10	chr22:29428000-29441800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr22:29428200-29430400	Enhancers	Liver	Liver
12	chr22:29428200-29434600	Genic enhancers	HepG2	liver
13	chr22:29428200-29436400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr22:29428400-29436400	Weak transcription	NHEK	skin
15	chr22:29428400-29436600	Weak transcription	K562	blood
16	chr22:29428600-29433200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr22:29428600-29440400	Weak transcription	Esophagus	oesophagus
18	chr22:29428600-29440800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr22:29428800-29433000	Weak transcription	Fetal Intestine Large	intestine
20	chr22:29428800-29436400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr22:29428800-29436400	Weak transcription	Left Ventricle	heart
22	chr22:29428800-29436600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr22:29428800-29436600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr22:29428800-29443600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr22:29429000-29430000	Enhancers	A549	lung
26	chr22:29429000-29430200	Strong transcription	Fetal Intestine Small	intestine
27	chr22:29429000-29432200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr22:29429000-29433000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr22:29429000-29433000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr22:29429000-29433200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr22:29429000-29433200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr22:29429000-29433600	Weak transcription	Placenta	Placenta
33	chr22:29429000-29435000	Weak transcription	Fetal Muscle Leg	muscle
34	chr22:29429000-29436400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr22:29429000-29436400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr22:29429000-29436400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr22:29429000-29436400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr22:29429000-29436400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr22:29429000-29436400	Weak transcription	Brain Anterior Caudate	brain
40	chr22:29429000-29436400	Weak transcription	Fetal Lung	lung
41	chr22:29429000-29436400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr22:29429000-29436400	Weak transcription	HSMMtube	muscle
43	chr22:29429000-29436600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr22:29429000-29436600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr22:29429000-29436600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr22:29429000-29436600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr22:29429000-29436600	Weak transcription	Fetal Kidney	kidney
48	chr22:29429000-29436600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr22:29429000-29436800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr22:29429000-29437000	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links