Variant report

Variant	rs11725878
Chromosome Location	chr4:91764098-91764099
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr4:91764073-91764510	HepG2	liver:	n/a	n/a
2	MYBL2	chr4:91763961-91764578	HepG2	liver:	n/a	n/a
3	FOXA2	chr4:91764080-91764462	HepG2	liver:	n/a	n/a
4	EBF1	chr4:91764096-91764531	GM12878	blood:	n/a	n/a
5	MAX	chr4:91764058-91764181	HepG2	liver:	n/a	n/a
6	STAT3	chr4:91763940-91764494	GM12878	blood:	n/a	n/a
7	BHLHE40	chr4:91764019-91764516	GM12878	blood:	n/a	n/a
8	MEF2A	chr4:91764033-91764459	GM12878	blood:	n/a	chr4:91764198-91764213 chr4:91764198-91764213 chr4:91764184-91764192
9	SP1	chr4:91764015-91764476	HepG2	liver:	n/a	n/a
10	EP300	chr4:91763903-91764565	GM12878	blood:	n/a	chr4:91763914-91763927
11	EP300	chr4:91764070-91764492	HepG2	liver:	n/a	n/a
12	EP300	chr4:91764030-91764491	HepG2	liver:	n/a	n/a
13	MEF2C	chr4:91764067-91764449	GM12878	blood:	n/a	chr4:91764198-91764213 chr4:91764198-91764213 chr4:91764184-91764192
14	FOXA1	chr4:91763934-91764542	HepG2	liver:	n/a	n/a
15	TBP	chr4:91763983-91764503	GM12878	blood:	n/a	n/a
16	ZNF384	chr4:91764085-91764598	GM12878	blood:	n/a	n/a
17	RCOR1	chr4:91763906-91764474	GM12878	blood:	n/a	n/a
18	EP300	chr4:91764054-91764480	GM12878	blood:	n/a	n/a
19	IKZF1	chr4:91763970-91764103	GM12878	blood:	n/a	chr4:91764024-91764032
20	TBL1XR1	chr4:91764049-91764455	GM12878	blood:	n/a	n/a
21	TEAD4	chr4:91764041-91764549	HepG2	liver:	n/a	n/a
22	IRF4	chr4:91764089-91764568	GM12878	blood:	n/a	n/a
23	BATF	chr4:91763992-91764477	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
TMSB4XP8	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10021524	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10022407	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11725824	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11936158	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs1304349	0.83[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap]
rs13132666	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13136779	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1377915	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs1902035	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2904373	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4643780	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4693247	0.87[GIH][hapmap]
rs6532250	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6854946	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9998356	0.87[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534470	chr4:91342219-91842807	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv428766	chr4:91618397-91768647	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv879553	chr4:91691313-91868576	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv879555	chr4:91743538-91967602	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv4422	chr4:91744177-91789188	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv491945	chr4:91753638-92240582	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11725878	DHX37	trans	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:91752400-91775000	Weak transcription	Pancreas	Pancrea
2	chr4:91754600-91771400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:91761600-91764600	Enhancers	HMEC	breast
4	chr4:91761600-91764600	Enhancers	NHEK	skin
5	chr4:91763000-91764600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:91763000-91766600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:91763400-91765000	Enhancers	HepG2	liver
8	chr4:91763600-91764400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:91763600-91764600	Enhancers	Fetal Intestine Small	intestine
10	chr4:91763800-91764200	Enhancers	A549	lung
11	chr4:91763800-91764400	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr4:91763800-91764600	Enhancers	Fetal Intestine Large	intestine
13	chr4:91763800-91766600	Weak transcription	HUVEC	blood vessel

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