Variant report

Variant	rs12240654
Chromosome Location	chr10:49923131-49923132
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11101432	1.00[CEU][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11101436	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12240581	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12245739	1.00[CEU][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12254896	1.00[CEU][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12266115	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12267792	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011056	0.85[EUR][1000 genomes]
rs17011111	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs17011119	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2377624	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs4838639	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs55668791	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7912944	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9971048	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1049259	chr10:49901984-49924310	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	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

No data

Chromatin state (count:14 , 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	chr10:49921000-49923600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr10:49921400-49923200	Genic enhancers	Primary B cells from cord blood	blood
5	chr10:49921400-49923400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
6	chr10:49921600-49923400	ZNF genes & repeats	GM12878-XiMat	blood
7	chr10:49921800-49923200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr10:49921800-49923600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr10:49922000-49933800	Weak transcription	Right Atrium	heart
10	chr10:49922200-49923400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr10:49922400-49923400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
12	chr10:49922800-49923400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
13	chr10:49922800-49923400	ZNF genes & repeats	Spleen	Spleen
14	chr10:49923000-49923400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood

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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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