Variant report

Variant	rs12045520
Chromosome Location	chr1:58085780-58085781
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11207081	0.82[CHB][hapmap]
rs11578358	0.80[CHB][hapmap]
rs11588804	0.80[CHB][hapmap]
rs12022839	0.80[CHB][hapmap]
rs12029004	0.80[CHB][hapmap]
rs12038397	0.80[CHB][hapmap]
rs12085345	0.80[CHB][hapmap]
rs1404384	0.80[CHB][hapmap]
rs1524707	0.80[CHB][hapmap]
rs1539053	0.80[CHB][hapmap]
rs1983454	0.80[CHB][hapmap]
rs7544337	0.80[CHB][hapmap]
rs7548317	0.80[CHB][hapmap]
rs7548624	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1012555	chr1:57950355-58103389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv530017	chr1:58002290-58669736	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv523574	chr1:58018103-58087789	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv871684	chr1:58021206-58096379	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12045520	NFIA	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58066000-58089000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:58066400-58089400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:58081200-58090600	Enhancers	Fetal Heart	heart
4	chr1:58081600-58089800	Enhancers	Fetal Muscle Leg	muscle
5	chr1:58081800-58086400	Weak transcription	Right Atrium	heart
6	chr1:58083000-58086400	Weak transcription	Spleen	Spleen
7	chr1:58083200-58086200	Weak transcription	Left Ventricle	heart
8	chr1:58083400-58088800	Weak transcription	HSMMtube	muscle
9	chr1:58084800-58086800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:58085200-58086600	Enhancers	Fetal Muscle Trunk	muscle
11	chr1:58085400-58086800	Enhancers	Right Ventricle	heart
12	chr1:58085400-58093600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:58085600-58086800	Enhancers	ES-UCSF4 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

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