Variant report

Variant	rs7623466
Chromosome Location	chr3:42414904-42414905
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11713695	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13340160	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1442272	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs247411	1.00[ASN][1000 genomes]
rs2907773	1.00[ASN][1000 genomes]
rs33506	1.00[ASN][1000 genomes]
rs33507	1.00[ASN][1000 genomes]
rs33508	1.00[ASN][1000 genomes]
rs33509	1.00[ASN][1000 genomes]
rs33512	1.00[ASN][1000 genomes]
rs33513	1.00[ASN][1000 genomes]
rs61083637	1.00[ASN][1000 genomes]
rs62248806	1.00[ASN][1000 genomes]
rs62248843	1.00[ASN][1000 genomes]
rs62248845	1.00[ASN][1000 genomes]
rs62257797	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73065860	0.82[AMR][1000 genomes]
rs735088	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529987	chr3:41921995-42591771	Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1009125	chr3:41953873-42472253	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv536549	chr3:41953873-42472253	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7623466	ZNF445	cis	cerebellum	SCAN
rs7623466	SCN10A	cis	parietal	SCAN
rs7623466	MOBP	cis	cerebellum	SCAN
rs7623466	ZNF167	cis	cerebellum	SCAN
rs7623466	ZNF501	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42411400-42415000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:42411400-42415000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:42411400-42415400	Weak transcription	Right Atrium	heart
4	chr3:42411400-42416200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:42411400-42420600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:42411600-42419800	Weak transcription	Brain Germinal Matrix	brain
7	chr3:42412000-42415000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:42412800-42416200	Weak transcription	Placenta	Placenta
9	chr3:42413600-42417200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:42414200-42415000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:42414200-42416000	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr3:42414200-42416200	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr3:42414400-42416200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:42414400-42416800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:42414600-42415000	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:42414600-42415800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:42414800-42415000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:42414800-42416000	Weak transcription	Primary monocytes fromperipheralblood	blood

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