Variant report

Variant	rs6791526
Chromosome Location	chr3:43256744-43256745
allele	C/T
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	chr3:43256070-43256757	T-47D	breast:	n/a	chr3:43256344-43256353
2	ESR1	chr3:43255981-43256780	T-47D	breast:	n/a	n/a
3	MAX	chr3:43256138-43256872	MCF-7	breast:	n/a	n/a
4	HA-E2F1	chr3:43256038-43256765	MCF-7	breast:	n/a	n/a
5	GATA3	chr3:43255990-43256766	MCF-7	breast:	n/a	chr3:43256344-43256353
6	ESR1	chr3:43255962-43256761	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:43233608..43236021-chr3:43256055..43258322,2	MCF-7	breast:
2	chr3:43226507..43227731-chr3:43255831..43257041,6	MCF-7	breast:
3	chr3:43235922..43238512-chr3:43256089..43258366,2	K562	blood:
4	chr3:43254448..43258211-chr3:43258239..43261327,4	K562	blood:
5	chr3:43226566..43227731-chr3:43255831..43257041,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222331	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs12486205	0.91[ASN][1000 genomes]
rs1317402	0.95[EUR][1000 genomes]
rs1318453	0.97[ASN][1000 genomes]
rs1320160	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1320161	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1320162	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1320163	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17075328	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17075340	1.00[ASN][1000 genomes]
rs17075375	0.94[ASN][1000 genomes]
rs17075379	0.94[ASN][1000 genomes]
rs17075391	0.94[ASN][1000 genomes]
rs17075395	0.91[ASN][1000 genomes]
rs17075415	0.95[EUR][1000 genomes]
rs17254504	0.96[EUR][1000 genomes]
rs17254786	0.96[EUR][1000 genomes]
rs17320570	0.96[EUR][1000 genomes]
rs17405916	0.85[EUR][1000 genomes]
rs1878721	0.94[ASN][1000 genomes]
rs1996497	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2372350	0.96[EUR][1000 genomes]
rs2372351	0.96[EUR][1000 genomes]
rs2372360	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2372361	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2372367	1.00[ASN][1000 genomes]
rs4504148	0.96[EUR][1000 genomes]
rs4682883	1.00[JPT][hapmap]
rs55650554	0.96[EUR][1000 genomes]
rs55836177	0.82[EUR][1000 genomes]
rs55919553	0.94[EUR][1000 genomes]
rs55988644	0.96[EUR][1000 genomes]
rs55990908	0.96[EUR][1000 genomes]
rs56032317	0.98[EUR][1000 genomes]
rs56053383	0.98[EUR][1000 genomes]
rs56291522	0.96[EUR][1000 genomes]
rs56412846	0.95[EUR][1000 genomes]
rs56745072	0.96[EUR][1000 genomes]
rs57757985	0.96[EUR][1000 genomes]
rs58504881	0.98[EUR][1000 genomes]
rs60971695	0.94[EUR][1000 genomes]
rs6766079	0.96[EUR][1000 genomes]
rs6767019	0.95[EUR][1000 genomes]
rs6791341	0.96[EUR][1000 genomes]
rs6796424	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs6798292	0.82[ASN][1000 genomes]
rs6800990	0.91[ASN][1000 genomes]
rs6801151	0.90[EUR][1000 genomes]
rs6805108	0.96[EUR][1000 genomes]
rs6808396	0.93[EUR][1000 genomes]
rs73072908	0.96[EUR][1000 genomes]
rs73072912	0.97[EUR][1000 genomes]
rs73072920	0.94[EUR][1000 genomes]
rs73086702	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088703	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088726	0.97[EUR][1000 genomes]
rs73088732	0.96[EUR][1000 genomes]
rs73088738	0.96[EUR][1000 genomes]
rs73088748	0.97[EUR][1000 genomes]
rs73088757	0.96[EUR][1000 genomes]
rs73829200	0.96[EUR][1000 genomes]
rs7633546	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7634209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641590	0.97[EUR][1000 genomes]
rs7646966	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7647227	0.97[ASN][1000 genomes]
rs938918	1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834672	chr3:43132722-43306272	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6791526	FYCO1	cis	parietal	SCAN
rs6791526	PTH1R	cis	cerebellum	SCAN
rs6791526	SNRK	cis	cerebellum	SCAN
rs6791526	PTH1R	cis	parietal	SCAN
rs6791526	SLC25A38	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43245000-43258800	Weak transcription	Right Atrium	heart
2	chr3:43247800-43259000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:43253200-43262400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr3:43253400-43259000	Weak transcription	Spleen	Spleen
5	chr3:43253600-43257400	Weak transcription	Left Ventricle	heart
6	chr3:43254000-43257000	Enhancers	Fetal Intestine Small	intestine
7	chr3:43254000-43257200	Enhancers	HMEC	breast
8	chr3:43254000-43258000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:43254200-43257800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:43254400-43256800	Enhancers	Fetal Intestine Large	intestine
11	chr3:43254400-43257200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:43255800-43257000	Enhancers	Duodenum Mucosa	Duodenum
13	chr3:43256000-43257000	Flanking Active TSS	NHEK	skin
14	chr3:43256200-43266800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr3:43256200-43267000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr3:43256400-43257000	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr3:43256400-43257200	Enhancers	Stomach Mucosa	stomach
18	chr3:43256400-43257800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:43256400-43257800	Enhancers	Pancreas	Pancrea
20	chr3:43256600-43256800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:43256600-43260600	Weak transcription	Fetal Kidney	kidney
22	chr3:43256600-43264000	Enhancers	Primary T cells from cord blood	blood

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