Variant report

Variant	rs960082
Chromosome Location	chr3:116017736-116017737
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs13066016	0.97[EUR][1000 genomes]
rs13069169	0.81[EUR][1000 genomes]
rs13079395	0.85[TSI][hapmap]
rs13083485	0.94[EUR][1000 genomes]
rs13084538	0.97[EUR][1000 genomes]
rs13089283	0.97[EUR][1000 genomes]
rs13089698	0.97[EUR][1000 genomes]
rs13090417	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13100898	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1346944	1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs16824766	0.97[EUR][1000 genomes]
rs17645807	1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs17647031	0.85[TSI][hapmap]
rs17702560	0.97[EUR][1000 genomes]
rs17702806	0.97[EUR][1000 genomes]
rs34126529	0.86[EUR][1000 genomes]
rs34279063	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34408946	0.91[EUR][1000 genomes]
rs34905742	0.91[EUR][1000 genomes]
rs35049642	0.96[ASN][1000 genomes]
rs35538266	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35966018	0.94[EUR][1000 genomes]
rs4831139	0.85[TSI][hapmap]
rs71323438	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71323439	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7645165	1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877360	chr3:115916171-116023990	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv3957	chr3:115986950-116032625	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs960082	LSAMP	cis	lymphoblastoid	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:116009000-116018600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:116009200-116018200	Weak transcription	Brain Germinal Matrix	brain
3	chr3:116014800-116018000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:116014800-116018000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:116015000-116017800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:116015000-116018000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:116015200-116017800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:116015400-116020800	Weak transcription	Fetal Lung	lung
9	chr3:116016800-116017800	Enhancers	Brain Hippocampus Middle	brain
10	chr3:116016800-116018400	Enhancers	Brain Cingulate Gyrus	brain
11	chr3:116016800-116018600	Enhancers	Brain Angular Gyrus	brain
12	chr3:116016800-116019600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr3:116017000-116029600	Enhancers	Colon Smooth Muscle	Colon
14	chr3:116017200-116018200	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr3:116017200-116020800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:116017400-116017800	Weak transcription	Brain Anterior Caudate	brain
17	chr3:116017400-116017800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:116017400-116017800	Weak transcription	Brain Substantia Nigra	brain
19	chr3:116017400-116019400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:116017600-116017800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:116017600-116019000	Enhancers	HUES48 Cell Line	embryonic stem cell

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