Variant report

Variant	rs71600499
Chromosome Location	chr4:121635598-121635599
allele	C/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	GATA3	chr4:121635412-121636196	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr4:121635552-121636104	MCF-7	breast:	n/a	n/a
3	CEBPB	chr4:121635451-121636206	Hela-S3	cervix:	n/a	n/a
4	TCF7L2	chr4:121635458-121636095	MCF-7	breast:	n/a	n/a
5	GATA3	chr4:121635596-121636074	MCF-7	breast:	n/a	n/a
6	TCF7L2	chr4:121635555-121636060	Hela-S3	cervix:	n/a	n/a
7	NR2F2	chr4:121635589-121636084	MCF-7	breast:	n/a	n/a
8	GATA3	chr4:121635450-121636166	SK-N-SH	brain:	n/a	n/a
9	EP300	chr4:121635461-121636094	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr4:121635551-121635614	MCF10A-Er-Src	breast:	n/a	n/a
11	TCF12	chr4:121635502-121636095	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:121633676..121636146-chr4:121637384..121639291,2	K562	blood:

Variant related genes	Relation type
PRDM5	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11721741	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11721810	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11721869	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11730092	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11732068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11732180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11736461	0.95[ASN][1000 genomes]
rs13145830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1397775	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17345994	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34414268	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34616798	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34631575	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34709185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35349319	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35418908	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35445561	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35576528	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36003774	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4833668	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60544114	0.90[AFR][1000 genomes]
rs6841589	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71600494	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71600495	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71600496	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71600500	0.95[ASN][1000 genomes]

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	nsv879852	chr4:121108734-121768496	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1004485	chr4:121542992-121716769	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv916737	chr4:121589793-121748847	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv461634	chr4:121623057-121765527	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv595334	chr4:121623057-121765527	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:121620800-121637600	Weak transcription	Psoas Muscle	Psoas
2	chr4:121620800-121654400	Weak transcription	Left Ventricle	heart
3	chr4:121620800-121671400	Weak transcription	Pancreas	Pancrea
4	chr4:121625600-121657600	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr4:121626000-121658200	Weak transcription	Aorta	Aorta
6	chr4:121629600-121643400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr4:121630000-121671400	Weak transcription	Ovary	ovary
8	chr4:121631600-121641200	Weak transcription	Fetal Heart	heart
9	chr4:121631800-121642200	Weak transcription	Fetal Lung	lung
10	chr4:121634000-121642400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr4:121635000-121636000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:121635400-121635800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:121635400-121636800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links