Variant report

Variant	rs13438587
Chromosome Location	chr7:47805513-47805514
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	chr7:47620351..47622930-chr7:47803514..47805956,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C7orf69-1	chr7:47805427-47806370	ENSG00000146666.4
2	lnc-C7orf69-1	chr7:47805427-47806369	ENSG00000146666.4

Variant related genes	Relation type
ENSG00000136205	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10085627	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10255459	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11971419	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11978262	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533948	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1466203	0.84[CEU][hapmap]
rs1551278	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17172902	0.83[ASW][hapmap];0.88[LWK][hapmap];0.87[MKK][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs17172903	0.89[AFR][1000 genomes]
rs28454924	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28581988	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28620363	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4720616	0.84[CEU][hapmap]
rs6953931	0.83[AFR][1000 genomes]
rs6968057	0.90[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6971770	0.83[AFR][1000 genomes]
rs7806630	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv888003	chr7:47694270-47907214	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1018608	chr7:47708525-47831535	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1022906	chr7:47709936-47831535	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv1015163	chr7:47734913-47832389	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv538831	chr7:47734913-47832389	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv830990	chr7:47767540-47837584	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13438587	HUS1	cis	parietal	SCAN
rs13438587	PURB	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47798600-47812200	Weak transcription	Aorta	Aorta
2	chr7:47802200-47805800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr7:47803000-47806200	Enhancers	HepG2	liver
4	chr7:47803200-47805600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr7:47803200-47807400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr7:47803400-47805600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr7:47803400-47805800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:47803600-47805600	Weak transcription	Colon Smooth Muscle	Colon
9	chr7:47803600-47806000	Enhancers	Hela-S3	cervix
10	chr7:47803600-47810400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:47803600-47810600	Weak transcription	HUVEC	blood vessel
12	chr7:47803800-47805800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr7:47804200-47805600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr7:47804200-47806200	Enhancers	Fetal Lung	lung
15	chr7:47804400-47807000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr7:47804400-47807000	Weak transcription	NH-A	brain
17	chr7:47804800-47811600	Weak transcription	Fetal Intestine Large	intestine
18	chr7:47805000-47810200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr7:47805200-47805800	Enhancers	Fetal Stomach	stomach
20	chr7:47805400-47805600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr7:47805400-47805600	Enhancers	Stomach Smooth Muscle	stomach
22	chr7:47805400-47805800	Flanking Active TSS	A549	lung
23	chr7:47805400-47806200	Enhancers	NHLF	lung
24	chr7:47805400-47811000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links