Variant report

Variant	rs17646052
Chromosome Location	chr3:116030986-116030987
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11918762	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs13073491	1.00[CHB][hapmap]
rs13321959	1.00[JPT][hapmap]
rs16824799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1712999	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs17702596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17704285	0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1835672	0.92[ASN][1000 genomes]
rs4831093	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6438312	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs6775293	1.00[CHB][hapmap]
rs6809953	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs72950135	0.96[ASN][1000 genomes]
rs957783	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs9811136	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9822049	0.92[ASN][1000 genomes]
rs9869252	1.00[JPT][hapmap]
rs9877364	0.83[CHD][hapmap];1.00[JPT][hapmap]

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	nsv3957	chr3:115986950-116032625	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv877361	chr3:116017931-116138039	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17646052	NR1I2	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:116019600-116037000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:116022200-116033000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:116026000-116031600	Weak transcription	Brain Angular Gyrus	brain
4	chr3:116026000-116031600	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:116026200-116037200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:116026400-116034000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:116028200-116037400	Weak transcription	Brain Germinal Matrix	brain
8	chr3:116028800-116031600	Weak transcription	Brain Substantia Nigra	brain
9	chr3:116028800-116033200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:116029200-116031400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:116029200-116031600	Weak transcription	Brain Anterior Caudate	brain
12	chr3:116029400-116031400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:116029400-116032800	Weak transcription	K562	blood
14	chr3:116029400-116033400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:116029600-116032200	Weak transcription	Colon Smooth Muscle	Colon

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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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