Variant report

Variant	rs1999498
Chromosome Location	chr9:101308111-101308112
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10986708	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10986740	0.84[CEU][hapmap]
rs12338626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12349351	0.93[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16917019	0.82[YRI][hapmap]
rs2001993	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2779600	0.92[YRI][hapmap]
rs2779602	0.94[ASW][hapmap];0.88[CEU][hapmap];0.81[GIH][hapmap];0.84[LWK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs884888	0.81[ASW][hapmap];0.84[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.81[EUR][1000 genomes]

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	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv831665	chr9:101170061-101367692	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	esv3481710	chr9:101307131-101313629	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
5	esv1804950	chr9:101307334-101311079	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
6	esv3497312	chr9:101307881-101312729	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
7	esv1849640	chr9:101308111-101311079	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
8	nsv511424	chr9:101308111-101313371	Bivalent Enhancer Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1999498	BARX1	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101304400-101311800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr9:101307200-101308200	Enhancers	Cortex derived primary cultured neurospheres	brain

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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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