Variant report

Variant	rs859996
Chromosome Location	chr9:105604461-105604462
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10117096	0.96[ASN][1000 genomes]
rs1099165	0.84[EUR][1000 genomes]
rs1342895	0.84[EUR][1000 genomes]
rs1352978	0.83[EUR][1000 genomes]
rs2797631	0.83[EUR][1000 genomes]
rs2797638	0.84[EUR][1000 genomes]
rs2812594	0.82[EUR][1000 genomes]
rs2812597	0.83[EUR][1000 genomes]
rs4743595	0.96[ASN][1000 genomes]
rs843261	0.85[EUR][1000 genomes]
rs843263	0.87[AFR][1000 genomes]
rs843264	0.82[AFR][1000 genomes]
rs843265	0.88[AFR][1000 genomes]
rs843266	0.85[EUR][1000 genomes]
rs843269	0.87[AFR][1000 genomes]
rs843270	0.84[AFR][1000 genomes]
rs843271	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047080	chr9:105432479-105658235	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv540185	chr9:105432479-105658235	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1054263	chr9:105570212-105754741	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv893655	chr9:105583926-105620803	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv430086	chr9:105585487-105632182	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1054932	chr9:105585667-105646429	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1053435	chr9:105594399-105733795	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs859996	COL15A1	cis	cerebellum	SCAN
rs859996	INVS	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:105602400-105606800	Enhancers	Fetal Intestine Small	intestine
2	chr9:105602600-105605200	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr9:105602600-105605400	Enhancers	Liver	Liver
4	chr9:105603400-105605200	Enhancers	HepG2	liver
5	chr9:105603600-105604800	Active TSS	Duodenum Mucosa	Duodenum
6	chr9:105604200-105607800	Enhancers	Fetal Intestine Large	intestine
7	chr9:105604400-105605200	Enhancers	A549	lung

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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