Variant report

Variant	rs1316952
Chromosome Location	chr12:124399550-124399551
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1048497	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs10744163	1.00[CHD][hapmap]
rs12424538	1.00[ASN][1000 genomes]
rs34934281	1.00[ASN][1000 genomes]
rs73424827	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv1811815	chr12:124374716-124424636	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv1832870	chr12:124374716-124424636	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv522321	chr12:124383950-124424636	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv560507	chr12:124395931-124400278	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv560514	chr12:124395982-124399550	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv560515	chr12:124395982-124400261	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv560527	chr12:124396135-124399550	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv560531	chr12:124396187-124400261	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
10	nsv560534	chr12:124396239-124399550	Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Visceral adipose tissue/subcutaneous adipose tissue ratio	22589738	GWAS catalog
Visceral adipose tissue adjusted for BMI	22589738	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1316952	P2RX7	cis	cerebellum	SCAN
rs1316952	ABCB9	cis	cerebellum	SCAN
rs1316952	SETD1B	cis	cerebellum	SCAN
rs1316952	TCTN2	cis	parietal	SCAN
rs1316952	P2RX4	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124384000-124408400	Weak transcription	Fetal Brain Female	brain
2	chr12:124393800-124418000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:124394200-124400200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:124394200-124418400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:124397600-124404800	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:124398000-124400000	Weak transcription	Spleen	Spleen
7	chr12:124398000-124402800	Weak transcription	Fetal Brain Male	brain
8	chr12:124398800-124399600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:124399000-124399800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:124399000-124400000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:124399000-124400800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:124399400-124399600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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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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