Variant report

Variant	rs1292646
Chromosome Location	chr1:10919094-10919095
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1152732	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1152733	0.96[AMR][1000 genomes]
rs539297	0.84[EUR][1000 genomes]
rs549925	0.92[AMR][1000 genomes]
rs550887	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs552630	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs592431	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs622120	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs637037	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529981	chr1:10697093-11353487	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	esv2757723	chr1:10742502-11055147	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2758921	chr1:10742502-11055147	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv871617	chr1:10858746-10935232	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv871155	chr1:10858746-10998509	Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv1825837	chr1:10887923-11093741	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv832425	chr1:10903845-11122975	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv545406	chr1:10915507-10935232	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1292646	NPPA	cis	parietal	SCAN
rs1292646	UBE4B	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10914000-10920800	Weak transcription	Gastric	stomach
2	chr1:10915600-10919400	Enhancers	Fetal Muscle Leg	muscle
3	chr1:10917400-10919600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:10917400-10921600	Weak transcription	Right Atrium	heart
5	chr1:10918200-10919200	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr1:10918200-10919800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:10918600-10920400	Weak transcription	Right Ventricle	heart
8	chr1:10918600-10920600	Weak transcription	Fetal Heart	heart
9	chr1:10918600-10920600	Weak transcription	Left Ventricle	heart
10	chr1:10918600-10923000	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr1:10918600-10926600	Weak transcription	Esophagus	oesophagus
12	chr1:10918800-10920600	Weak transcription	Psoas Muscle	Psoas
13	chr1:10918800-10920800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:10919000-10920800	Enhancers	Skeletal Muscle Male	skeletal muscle

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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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