Variant report

Variant	rs404238
Chromosome Location	chr6:14848468-14848469
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12189594	0.89[EUR][1000 genomes]
rs233496	0.80[AMR][1000 genomes]
rs372827	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs384291	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs411347	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs449159	0.81[CEU][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs452951	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4715928	0.89[EUR][1000 genomes]
rs6459378	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6459379	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7755454	0.95[ASN][1000 genomes]
rs865082	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[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	nsv1031668	chr6:14774036-15044308	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv538138	chr6:14774036-15044308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1017572	chr6:14830510-14906933	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs404238	CAP2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:14832200-14855400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:14839600-14849400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr6:14843600-14850200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:14844000-14849600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:14845200-14850400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:14847000-14855400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:14848000-14848600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:14848000-14848600	Enhancers	HSMM	muscle
9	chr6:14848000-14849200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:14848000-14850600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:14848200-14848800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:14848200-14849200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:14848400-14848600	Enhancers	H1 Cell Line	embryonic stem cell
14	chr6:14848400-14849400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:14848400-14850400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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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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