Variant report

Variant	rs745580
Chromosome Location	chr7:26008052-26008053
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:25989287..25991159-chr7:26005525..26008414,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000199085	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10236909	0.89[EUR][1000 genomes]
rs10267354	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11981669	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13239817	0.94[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs17152959	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2012224	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2893234	0.89[EUR][1000 genomes]
rs35153396	0.87[ASN][1000 genomes]
rs35931836	0.89[ASN][1000 genomes]
rs4521656	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4719845	0.89[EUR][1000 genomes]
rs4719848	0.86[EUR][1000 genomes]
rs6461900	0.90[EUR][1000 genomes]
rs6461902	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6461903	0.89[EUR][1000 genomes]
rs6947773	0.91[EUR][1000 genomes]
rs6958870	0.92[CEU][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6972351	0.81[ASN][1000 genomes]
rs733645	0.94[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs766838	0.89[EUR][1000 genomes]
rs7786527	0.94[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs7792195	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016813	chr7:25405859-26150509	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
2	nsv538803	chr7:25405859-26150509	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
3	nsv606432	chr7:25988185-26223294	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
4	nsv887848	chr7:26000137-26059739	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv606433	chr7:26007582-26050920	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Obesity-related traits	23251661	GWAS catalog

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26002800-26009000	Weak transcription	Right Atrium	heart
2	chr7:26006000-26009000	Flanking Active TSS	GM12878-XiMat	blood
3	chr7:26006200-26008800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr7:26006600-26008800	Enhancers	Pancreas	Pancrea
5	chr7:26006600-26009000	Enhancers	Fetal Muscle Leg	muscle
6	chr7:26007000-26008800	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr7:26007000-26008800	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr7:26007200-26008400	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr7:26007200-26008800	Enhancers	Spleen	Spleen
10	chr7:26007200-26009000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr7:26007200-26009200	Enhancers	Fetal Muscle Trunk	muscle
12	chr7:26007400-26008400	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr7:26007400-26008800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr7:26007400-26009600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr7:26007600-26008600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr7:26007800-26008400	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
17	chr7:26007800-26008400	Enhancers	Gastric	stomach
18	chr7:26007800-26008600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
19	chr7:26008000-26008200	Enhancers	HSMM	muscle
20	chr7:26008000-26008200	Enhancers	Osteobl	bone
21	chr7:26008000-26008400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
22	chr7:26008000-26008400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
23	chr7:26008000-26008600	Flanking Active TSS	Primary B cells from peripheral blood	blood
24	chr7:26008000-26008600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
25	chr7:26008000-26008600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr7:26008000-26008600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links