Variant report

Variant	rs2523443
Chromosome Location	chr6:29415464-29415465
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs1233480	0.86[EUR][1000 genomes]
rs1233493	0.98[EUR][1000 genomes]
rs1233494	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1234844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2023463	0.98[EUR][1000 genomes]
rs2143668	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2523431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2523432	0.92[EUR][1000 genomes]
rs2746149	0.98[EUR][1000 genomes]
rs2746150	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3094569	0.89[EUR][1000 genomes]
rs404240	0.91[EUR][1000 genomes]
rs408623	0.91[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	nsv830624	chr6:29274525-29445565	Enhancers Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	esv15709	chr6:29413527-29415648	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2523443	HIST1H2BC	cis	parietal	SCAN
rs2523443	HLA-H	cis	multi-tissue	Pritchard
rs2523443	HIST1H2BM	cis	cerebellum	SCAN
rs2523443	BTN3A2	cis	multi-tissue	Pritchard
rs2523443	HLA-A	trans	brain	seeQTL
rs2523443	ZNF323	cis	parietal	SCAN
rs2523443	BTN3A2	trans	lymphoblastoid	seeQTL
rs2523443	HLA-C	cis	multi-tissue	Pritchard
rs2523443	HLA-G	cis	multi-tissue	Pritchard
rs2523443	HLA-A	cis	multi-tissue	Pritchard
rs2523443	HLA-A	cis	brain	seeQTL
rs2523443	BTN2A1	cis	parietal	SCAN
rs2523443	ZFP57	cis	multi-tissue	Pritchard

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29413400-29415600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:29414200-29416000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:29414200-29418000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:29414600-29415600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr6:29415000-29415600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr6:29415000-29415600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:29415000-29415800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:29415200-29415600	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr6:29415200-29415600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr6:29415200-29415600	Enhancers	NHEK	skin
11	chr6:29415200-29416200	Enhancers	HMEC	breast

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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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