Variant report

Variant	rs10857624
Chromosome Location	chr10:49924467-49924468
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10458720	1.00[MKK][hapmap]
rs10776634	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10776635	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10776636	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10776637	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10776638	0.87[CEU][hapmap];0.95[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10857621	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10857622	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10857623	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11101431	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11101437	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1871610	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2377626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2889687	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7067842	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100075	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs7100103	0.87[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.80[AMR][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	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv895373	chr10:49911737-49933488	Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10857624	LOC338579	cis	cerebellum	SCAN
rs10857624	ROCK1P1	trans	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49913000-49930600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:49919800-49927800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr10:49922000-49933800	Weak transcription	Right Atrium	heart
4	chr10:49923200-49925200	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr10:49923400-49926400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr10:49923400-49927000	Strong transcription	GM12878-XiMat	blood
7	chr10:49923400-49928000	Weak transcription	Spleen	Spleen
8	chr10:49923400-49928400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr10:49923400-49932400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr10:49923400-49960200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr10:49923600-49924600	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr10:49923600-49927800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr10:49923600-49939400	Weak transcription	Adipose Nuclei	Adipose
14	chr10:49924200-49924600	Weak transcription	Primary B cells from cord blood	blood
15	chr10:49924200-49925200	Genic enhancers	Primary B cells from peripheral blood	blood

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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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