Variant report

Variant	rs7786527
Chromosome Location	chr7:26007582-26007583
allele	G/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: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs13239817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17152959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1986928	0.88[ASN][1000 genomes]
rs2012224	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35052122	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35055962	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35153396	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35797325	0.88[ASN][1000 genomes]
rs35855074	0.87[ASN][1000 genomes]
rs35931836	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4521656	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62446278	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6461901	0.88[ASN][1000 genomes]
rs6951118	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6972351	0.91[ASN][1000 genomes]
rs6973562	0.88[ASN][1000 genomes]
rs733645	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];0.99[ASN][1000 genomes]
rs745580	0.94[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs7792195	0.90[ASN][1000 genomes]
rs7803271	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7786527	FAM126A	cis	parietal	SCAN
rs7786527	HOXA4	cis	cerebellum	SCAN

Chromatin state (count:23 , 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	chr7:26006800-26007600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr7:26006800-26008000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr7:26006800-26008000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr7:26007000-26007800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
10	chr7:26007000-26008000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
11	chr7:26007000-26008800	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr7:26007000-26008800	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr7:26007200-26007800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr7:26007200-26008000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
15	chr7:26007200-26008400	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr7:26007200-26008800	Enhancers	Spleen	Spleen
17	chr7:26007200-26009000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr7:26007200-26009200	Enhancers	Fetal Muscle Trunk	muscle
19	chr7:26007400-26007800	Weak transcription	Gastric	stomach
20	chr7:26007400-26008000	Enhancers	Primary B cells from peripheral blood	blood
21	chr7:26007400-26008400	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr7:26007400-26008800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr7:26007400-26009600	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