Variant report

Variant	rs12239127
Chromosome Location	chr1:114617597-114617598
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10858029	0.88[EUR][1000 genomes]
rs11102720	0.84[EUR][1000 genomes]
rs11102724	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12066263	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12749841	0.82[ASN][1000 genomes]
rs12755538	0.81[EUR][1000 genomes]
rs12759829	0.81[EUR][1000 genomes]
rs1503835	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4839352	0.85[EUR][1000 genomes]
rs4839354	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4839355	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4839358	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4839359	0.89[EUR][1000 genomes]
rs61819248	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7521423	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv1849780	chr1:114577463-114663164	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv463284	chr1:114585590-114623867	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv547568	chr1:114585590-114623867	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv547569	chr1:114587766-114625425	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12239127	C1orf103	cis	cerebellum	SCAN
rs12239127	NGF	cis	cerebellum	SCAN
rs12239127	CSDE1	cis	cerebellum	SCAN
rs12239127	ST7L	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114615000-114618800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:114615800-114617600	Weak transcription	Fetal Muscle Leg	muscle
3	chr1:114616800-114620200	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr1:114617000-114617600	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr1:114617000-114618400	Enhancers	H9 Cell Line	embryonic stem cell
6	chr1:114617200-114619600	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr1:114617200-114620200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr1:114617200-114620200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr1:114617400-114617800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr1:114617400-114618200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:114617400-114618800	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr1:114617400-114618800	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr1:114617400-114618800	Enhancers	Fetal Lung	lung
14	chr1:114617400-114619600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr1:114617400-114620200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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