Variant report

Variant	rs10876838
Chromosome Location	chr12:56030938-56030939
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10783763	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10876834	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11171639	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34372941	0.81[AMR][1000 genomes]
rs34817228	0.81[AMR][1000 genomes]
rs3847676	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7309433	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7954307	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7967574	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7970885	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978340	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559001	chr12:55507465-56057708	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv948625	chr12:55838718-56118833	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3490751	chr12:56030785-56035633	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10876838	KRT18	cis	parietal	SCAN
rs10876838	SUOX	cis	parietal	SCAN
rs10876838	MMP19	cis	cerebellum	SCAN
rs10876838	OR9K2	cis	cerebellum	SCAN
rs10876838	DCD	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56023200-56036800	Weak transcription	Spleen	Spleen
2	chr12:56025800-56035200	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr12:56030200-56031000	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr12:56030400-56031000	Enhancers	Left Ventricle	heart
5	chr12:56030400-56031000	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr12:56030600-56031400	Enhancers	Primary T cells fromperipheralblood	blood
7	chr12:56030600-56032600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:56030800-56031000	Enhancers	Esophagus	oesophagus
9	chr12:56030800-56031200	Enhancers	Right Atrium	heart
10	chr12:56030800-56035800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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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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