Variant report

Variant	rs13127517
Chromosome Location	chr4:120222883-120222884
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:5)
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	TCF7L2	chr4:120222701-120223247	HEK293	kidney:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:120132610..120134570-chr4:120221091..120222996,2	MCF-7	breast:
2	chr4:120132453..120136158-chr4:120220202..120223113,6	K562	blood:
3	chr4:120130951..120136158-chr4:120218006..120223072,8	K562	blood:
4	chr4:120220396..120223311-chr4:120987092..120990068,3	K562	blood:
5	chr20:55840161..55841677-chr4:120221342..120223626,2	MCF-7	breast:

No data

Variant related genes	Relation type
C4orf3	TF binding region
ENSG00000164109	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000250938	Chromatin interaction
ENSG00000145390	Chromatin interaction
ENSG00000178636	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs11722431	0.83[EUR][1000 genomes]
rs11722940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11724619	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11725409	0.83[EUR][1000 genomes]
rs11725433	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11728178	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11729960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11733606	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11734624	0.83[EUR][1000 genomes]
rs11734808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11736997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11737068	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11737560	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs13104050	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13106878	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs13112320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13113462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13113662	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13116789	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs13122306	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13124532	1.00[ASW][hapmap];0.93[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs13139711	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13140255	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13144426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1397611	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1511021	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1511022	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs17050312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17334151	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17517075	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17517470	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17595468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17595769	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17595790	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2036859	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34125807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34156358	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34478210	0.81[ASN][1000 genomes]
rs34624042	0.81[ASN][1000 genomes]
rs34733524	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34878806	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34951506	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35137697	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35225855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35612705	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35646004	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35830965	0.81[ASN][1000 genomes]
rs35846514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35917388	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3817230	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3817242	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56818816	0.86[ASN][1000 genomes]
rs62320715	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320716	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320717	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320718	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320719	0.81[ASN][1000 genomes]
rs62320720	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320721	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320722	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320723	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320724	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320725	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320731	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320732	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320733	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320735	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62320737	0.91[ASN][1000 genomes]
rs62322274	0.83[EUR][1000 genomes]
rs62322275	0.83[EUR][1000 genomes]
rs62322276	0.85[EUR][1000 genomes]
rs62328380	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62328402	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62328403	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62328404	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62328408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62328420	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6822097	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6846936	0.81[ASN][1000 genomes]
rs71610255	0.81[ASN][1000 genomes]
rs71627784	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72918504	0.84[EUR][1000 genomes];0.91[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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv428769	chr4:120205572-120363323	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13127517	USP53	cis	cerebellum	SCAN
rs13127517	USP53	cis	Whole Blood	GTEx
rs13127517	USP53	cis	parietal	SCAN
rs13127517	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs13127517	RP11-33B1.1	cis	Thyroid	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120220000-120223200	Active TSS	GM12878-XiMat	blood
2	chr4:120221800-120223000	Flanking Active TSS	Dnd41	blood
3	chr4:120222000-120251000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:120222200-120223400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr4:120222200-120223400	Weak transcription	HSMMtube	muscle
6	chr4:120222200-120223600	Enhancers	Fetal Heart	heart
7	chr4:120222200-120244600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:120222400-120227800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr4:120222400-120229000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr4:120222400-120240800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:120222600-120223000	Enhancers	Brain Cingulate Gyrus	brain
12	chr4:120222600-120223000	Flanking Active TSS	HepG2	liver
13	chr4:120222600-120223200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:120222600-120223200	Enhancers	Fetal Intestine Large	intestine
15	chr4:120222600-120223400	Enhancers	Liver	Liver
16	chr4:120222600-120224800	Weak transcription	Fetal Intestine Small	intestine
17	chr4:120222800-120224000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr4:120222800-120240800	Weak transcription	Rectal Mucosa Donor 31	rectum

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