Variant report

Variant	rs1868348
Chromosome Location	chr2:33925829-33925830
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1448556	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1550992	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1900775	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55826931	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6543736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6543738	0.83[EUR][1000 genomes]
rs6543739	0.83[EUR][1000 genomes]
rs6715757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7562867	0.88[ASN][1000 genomes]
rs7574123	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[ASN][1000 genomes]
rs7581496	0.96[ASN][1000 genomes]
rs7585657	0.88[CEU][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs7588769	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	esv3350238	chr2:33849408-33979026	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3437071	chr2:33923648-33927946	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
3	esv3456894	chr2:33924498-33926996	ZNF genes & repeats Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
4	esv3456895	chr2:33924498-33926996	Weak transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1868348	HSH2D	trans	parietal	SCAN
rs1868348	FAM98A	cis	cerebellum	SCAN
rs1868348	TTC27	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33923000-33929200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:33925000-33929400	Weak transcription	Right Ventricle	heart
3	chr2:33925600-33926000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:33925600-33926000	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell

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