Variant report

Variant	rs1233480
Chromosome Location	chr6:29477414-29477415
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1233493	0.84[EUR][1000 genomes]
rs1233494	0.84[EUR][1000 genomes]
rs1234844	0.84[EUR][1000 genomes]
rs2023463	0.84[EUR][1000 genomes]
rs2143668	0.86[EUR][1000 genomes]
rs2523431	0.86[EUR][1000 genomes]
rs2523432	0.94[EUR][1000 genomes]
rs2523443	0.86[EUR][1000 genomes]
rs2746149	0.84[EUR][1000 genomes]
rs2746150	0.86[EUR][1000 genomes]
rs3094569	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3424039	chr6:29439297-29504564	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv883528	chr6:29447724-29494897	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv883529	chr6:29464365-29494897	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1233480	HIST1H2BC	cis	parietal	SCAN
rs1233480	HLA-C	Cis_chr	lymphoblastoid	RTeQTL
rs1233480	ZNF323	cis	parietal	SCAN
rs1233480	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs1233480	HIST1H2BM	cis	cerebellum	SCAN
rs1233480	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs1233480	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs1233480	BTN2A1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29468600-29496200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:29475200-29477800	Enhancers	GM12878-XiMat	blood
3	chr6:29476800-29481600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:29477400-29478800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:29477400-29478800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:29477400-29478800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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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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