Variant report

Variant	rs2377625
Chromosome Location	chr10:49921303-49921304
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11594765	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11597850	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17011111	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17698635	0.82[CEU][hapmap]
rs17771282	0.82[CEU][hapmap]
rs17771443	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871608	0.94[ASW][hapmap];0.85[LWK][hapmap];0.87[MKK][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes]
rs1871609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1904601	0.94[ASW][hapmap];0.85[LWK][hapmap];0.87[MKK][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes]
rs2377624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838425	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7069001	0.94[ASW][hapmap];0.83[CEU][hapmap];0.80[LWK][hapmap];0.82[MKK][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes]
rs7069023	0.89[AFR][1000 genomes]
rs72787297	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7896204	0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs7912944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2377625	NDUFB9	trans	cerebellum	SCAN
rs2377625	WDFY4	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49908200-49922800	Weak transcription	Spleen	Spleen
2	chr10:49913000-49930600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:49914200-49922600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr10:49915400-49921600	Strong transcription	GM12878-XiMat	blood
5	chr10:49916800-49921600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr10:49916800-49921600	Weak transcription	Right Atrium	heart
7	chr10:49917800-49921400	Strong transcription	Primary B cells from cord blood	blood
8	chr10:49917800-49921400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr10:49917800-49921600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr10:49917800-49921800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr10:49917800-49922400	Strong transcription	Primary hematopoietic stem cells	blood
12	chr10:49918200-49922800	Strong transcription	Primary B cells from peripheral blood	blood
13	chr10:49918400-49922400	Enhancers	Left Ventricle	heart
14	chr10:49919600-49922000	Weak transcription	Right Ventricle	heart
15	chr10:49919800-49927800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr10:49920400-49922000	Enhancers	Fetal Heart	heart
17	chr10:49920600-49921800	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr10:49921000-49923600	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr10:49921200-49921400	Genic enhancers	Monocytes-CD14+_RO01746	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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