Variant report

Variant	rs1603000
Chromosome Location	chr1:84580593-84580594
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1021491	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10874427	1.00[CEU][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs12756327	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2250806	0.93[CEU][hapmap];0.83[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2642186	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2792973	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2792975	1.00[CEU][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2792976	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs594631	0.83[CEU][hapmap];0.90[EUR][1000 genomes]
rs599686	0.94[EUR][1000 genomes]
rs603939	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs617568	0.91[EUR][1000 genomes]
rs638545	0.90[EUR][1000 genomes]
rs648856	0.94[EUR][1000 genomes]
rs650629	0.90[EUR][1000 genomes]
rs652489	0.86[EUR][1000 genomes]
rs6576959	0.91[EUR][1000 genomes]
rs6701486	1.00[CEU][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][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	nsv546689	chr1:84531117-84670816	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv546690	chr1:84562265-84655238	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1603000	MCOLN2	cis	parietal	SCAN
rs1603000	LOC339524	cis	cerebellum	SCAN
rs1603000	BCL10	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84569000-84585000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:84569200-84581400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:84569200-84587400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:84569200-84599600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:84569400-84587400	Weak transcription	Ovary	ovary
6	chr1:84569800-84583600	Weak transcription	HSMM	muscle
7	chr1:84573800-84582400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:84574000-84583600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:84574000-84583600	Weak transcription	HMEC	breast
10	chr1:84574000-84587400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:84574800-84585600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:84576000-84591800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

Quick Search:

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

what's new

Quick links