Variant report

Variant	rs12823931
Chromosome Location	chr12:4467921-4467922
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10849040	0.82[CEU][hapmap]
rs11063112	0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[LWK][hapmap]
rs11063118	0.88[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs12229274	0.88[ASN][1000 genomes]
rs12230757	0.87[CHB][hapmap];1.00[LWK][hapmap]
rs13312789	0.86[CHB][hapmap];0.85[LWK][hapmap]
rs17773299	0.87[CHB][hapmap]
rs3812822	0.87[CHB][hapmap]
rs7133330	0.95[LWK][hapmap]
rs7316649	0.87[CHB][hapmap]
rs7955866	0.94[CHB][hapmap];0.95[LWK][hapmap]
rs7976548	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530520	chr12:3726841-4601757	Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv468985	chr12:4423612-4473329	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv557122	chr12:4423612-4473329	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	nsv557123	chr12:4436632-4736569	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv519278	chr12:4441906-4475194	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv528492	chr12:4462161-4473329	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv523578	chr12:4462505-4467921	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12823931	C12orf5	cis	cerebellum	SCAN
rs12823931	LRRC23	cis	parietal	SCAN
rs12823931	CLEC4A	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4462200-4468000	Weak transcription	Fetal Brain Female	brain
2	chr12:4462600-4468000	Weak transcription	Primary B cells from cord blood	blood
3	chr12:4462800-4468200	Weak transcription	GM12878-XiMat	blood
4	chr12:4463800-4468000	Weak transcription	HMEC	breast
5	chr12:4464000-4468600	Weak transcription	HUVEC	blood vessel
6	chr12:4464000-4469200	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr12:4464800-4468200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:4465200-4488400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:4465400-4474400	Weak transcription	Right Atrium	heart
10	chr12:4465400-4475200	Weak transcription	Gastric	stomach

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