Variant report

Variant	rs12465274
Chromosome Location	chr2:40615215-40615216
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10865163	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11124740	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12472012	0.91[ASN][1000 genomes]
rs12611557	0.90[ASN][1000 genomes]
rs12615002	0.89[ASN][1000 genomes]
rs2192774	0.91[AFR][1000 genomes]
rs56316253	0.86[ASN][1000 genomes]
rs57020706	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7557545	0.87[ASN][1000 genomes]
rs7570435	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2757794	chr2:40547947-40733776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2759044	chr2:40547947-40733776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv873915	chr2:40573350-40615520	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv1804767	chr2:40601179-40615520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv1805808	chr2:40601179-40615520	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv1805510	chr2:40604270-40615520	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv1813430	chr2:40604270-40615520	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv873916	chr2:40607504-40649084	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv9658	chr2:40612009-40615720	Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv1804337	chr2:40612072-40615520	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv1814051	chr2:40612072-40615520	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	esv1804911	chr2:40612347-40615520	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv1806109	chr2:40612347-40620150	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	esv1815130	chr2:40612347-40620150	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	esv2760574	chr2:40612784-40621110	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12465274	SLC8A1	cis	Whole Blood	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40601000-40621800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:40608400-40622000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr2:40609600-40621800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr2:40610000-40619000	Weak transcription	Dnd41	blood
5	chr2:40611400-40616200	Weak transcription	Left Ventricle	heart
6	chr2:40612600-40622600	Weak transcription	HSMM	muscle
7	chr2:40613000-40616000	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr2:40613000-40618800	Weak transcription	Colon Smooth Muscle	Colon
9	chr2:40613000-40619200	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr2:40613600-40617200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr2:40614000-40616200	Enhancers	Fetal Heart	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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