Variant report

Variant	rs17188506
Chromosome Location	chr1:210884083-210884084
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10494928	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11119571	0.81[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11119575	0.81[CHB][hapmap];0.95[GIH][hapmap];0.82[EUR][1000 genomes]
rs12122565	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];0.80[AMR][1000 genomes]
rs12123159	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12125545	0.91[JPT][hapmap];0.81[MKK][hapmap];0.81[AMR][1000 genomes]
rs12126038	0.83[AMR][1000 genomes]
rs12127398	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12140954	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12141923	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17188416	0.90[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];0.80[AMR][1000 genomes]
rs2226023	0.81[CHB][hapmap]
rs2357921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4628571	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs60195529	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv873148	chr1:210665583-210994339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv873150	chr1:210808270-210893233	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17188506	CR2	cis	parietal	SCAN
rs17188506	TRAF3IP3	cis	lymphoblastoid	seeQTL
rs17188506	C1orf107	cis	parietal	SCAN
rs17188506	G0S2	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210846400-210884600	Weak transcription	Ovary	ovary
2	chr1:210864400-210889800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:210866800-210884800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:210871200-210932000	Weak transcription	HSMM	muscle
5	chr1:210874200-210887400	Weak transcription	HSMMtube	muscle
6	chr1:210877200-210888400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:210879600-210884200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:210881800-210901200	Weak transcription	Brain Angular Gyrus	brain
9	chr1:210884000-210884200	Enhancers	Left Ventricle	heart

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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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