Variant report

Variant	rs1887295
Chromosome Location	chr1:184161013-184161014
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10752934	0.91[ASN][1000 genomes]
rs1078926	0.91[ASN][1000 genomes]
rs11582627	0.92[ASN][1000 genomes]
rs12123933	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136030	0.90[ASN][1000 genomes]
rs1327143	1.00[CHB][hapmap]
rs17574056	0.81[ASN][1000 genomes]
rs2025808	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2042556	0.85[ASN][1000 genomes]
rs59795179	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60072887	0.91[ASN][1000 genomes]
rs6684045	0.82[ASN][1000 genomes]
rs6690187	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67878484	0.81[ASN][1000 genomes]
rs7527771	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540770	1.00[CHB][hapmap]
rs997343	0.82[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	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1006655	chr1:183922288-184186677	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1887295	GLT25D2	cis	cerebellum	SCAN
rs1887295	STX6	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184157000-184162000	Weak transcription	Right Ventricle	heart
2	chr1:184157000-184162200	Weak transcription	Left Ventricle	heart
3	chr1:184157800-184162400	Enhancers	Fetal Heart	heart
4	chr1:184158600-184163200	Enhancers	Fetal Stomach	stomach
5	chr1:184159400-184161400	Enhancers	Fetal Lung	lung
6	chr1:184159600-184161600	Enhancers	Fetal Muscle Leg	muscle
7	chr1:184159800-184161400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:184160000-184161200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:184160000-184161200	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr1:184160000-184161200	Enhancers	NHLF	lung
11	chr1:184160200-184161200	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr1:184160600-184163200	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:184160800-184162600	Weak transcription	Fetal Brain Male	brain
14	chr1:184160800-184169200	Weak transcription	Fetal Brain Female	brain
15	chr1:184161000-184163200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:184161000-184165400	Weak transcription	HSMMtube	muscle
17	chr1:184161000-184168200	Weak transcription	Fetal Kidney	kidney

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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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