Variant report

Variant	rs10846578
Chromosome Location	chr12:124400278-124400279
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10846577	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10846579	0.84[ASN][1000 genomes]
rs10846580	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs11057393	0.84[ASN][1000 genomes]
rs11057394	1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs11057396	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs11057397	1.00[CHB][hapmap];0.83[CHD][hapmap];0.80[ASN][1000 genomes]
rs12298484	1.00[CHB][hapmap];0.83[CHD][hapmap];0.80[ASN][1000 genomes]
rs12317176	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs12322694	0.82[CHD][hapmap]
rs12809125	1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs3802999	1.00[CHB][hapmap];0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs4575361	0.84[ASN][1000 genomes]
rs4930721	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs7133378	1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[ASN][1000 genomes]
rs7301953	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.86[ASN][1000 genomes]
rs9863	1.00[CHB][hapmap]
rs9971695	1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[ASN][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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10846578	PITPNM2	cis	cerebellum	SCAN
rs10846578	TAOK1	trans	cerebellum	SCAN
rs10846578	CCDC92	cis	cerebellum	SCAN
rs10846578	EIF2B1	cis	cerebellum	SCAN

Chromatin state (count:9 , 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	chr12:124394200-124418400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr12:124397600-124404800	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr12:124398000-124402800	Weak transcription	Fetal Brain Male	brain
6	chr12:124399000-124400800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:124399800-124402000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:124400000-124400400	Enhancers	Spleen	Spleen
9	chr12:124400200-124400400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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