Variant report

Variant	rs10489958
Chromosome Location	chr1:221202662-221202663
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs17009184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009190	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009209	1.00[ASN][1000 genomes]
rs17009253	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17513397	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17573664	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36116663	1.00[ASN][1000 genomes]
rs41353047	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73097462	1.00[ASN][1000 genomes]
rs7515981	1.00[ASN][1000 genomes]
rs7536397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv873199	chr1:221136672-221451217	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10489958	MTTP	trans	brain	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221194400-221205600	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr1:221196400-221206600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:221196600-221205800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:221196800-221204600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:221196800-221205000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:221199200-221203000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:221199600-221203000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:221199600-221203000	Weak transcription	Fetal Muscle Leg	muscle
9	chr1:221199800-221203000	Weak transcription	Left Ventricle	heart
10	chr1:221199800-221209200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr1:221200000-221203000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:221200000-221204200	Weak transcription	Primary B cells from cord blood	blood
13	chr1:221202000-221205200	Enhancers	Colon Smooth Muscle	Colon
14	chr1:221202200-221205400	Enhancers	Rectal Smooth Muscle	rectum
15	chr1:221202400-221203200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr1:221202400-221205000	Enhancers	Fetal Stomach	stomach

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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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