Variant report

Variant	rs2187958
Chromosome Location	chr1:175110955-175110956
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10489327	0.91[MEX][hapmap]
rs10489328	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.97[ASN][1000 genomes]
rs1057285	0.89[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs12139941	0.91[MEX][hapmap]
rs16847872	0.91[MEX][hapmap]
rs1894708	0.91[ASN][1000 genomes]
rs2018318	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.96[ASN][1000 genomes]
rs2269655	0.91[MEX][hapmap]
rs2861157	0.97[ASN][1000 genomes]
rs3737933	0.83[GIH][hapmap];0.82[MEX][hapmap]
rs4651335	0.83[ASN][1000 genomes]
rs56237830	0.85[EUR][1000 genomes]
rs6679268	0.94[ASN][1000 genomes]
rs73032622	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv825487	chr1:175031609-175113572	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv508648	chr1:175056387-175121913	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv522101	chr1:175109517-175151183	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv429924	chr1:175110480-175134314	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2187958	SNORD79	cis	cerebellum	SCAN
rs2187958	KIAA0040	cis	multi-tissue	Pritchard
rs2187958	CACYBP	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175108000-175119800	Weak transcription	Adipose Nuclei	Adipose
2	chr1:175109600-175114000	Weak transcription	Liver	Liver
3	chr1:175110200-175127400	Weak transcription	Left Ventricle	heart
4	chr1:175110600-175111200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:175110600-175111600	Flanking Active TSS	GM12878-XiMat	blood
6	chr1:175110600-175112400	Enhancers	Primary B cells from peripheral blood	blood
7	chr1:175110800-175111200	Enhancers	Primary T cells from cord blood	blood
8	chr1:175110800-175111200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:175110800-175111600	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr1:175110800-175111800	Enhancers	Fetal Intestine Large	intestine
11	chr1:175110800-175111800	Enhancers	Fetal Intestine Small	intestine
12	chr1:175110800-175112400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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

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