Variant report

Variant	rs12747817
Chromosome Location	chr1:175118895-175118896
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1057301	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1057302	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1057305	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11580331	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11585617	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34493921	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6425323	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6659824	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6677097	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6681020	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6683533	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6701037	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6702010	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6929	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7512413	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7514749	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508648	chr1:175056387-175121913	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv522101	chr1:175109517-175151183	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv429924	chr1:175110480-175134314	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12747817	KIAA0040	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175108000-175119800	Weak transcription	Adipose Nuclei	Adipose
2	chr1:175110200-175127400	Weak transcription	Left Ventricle	heart
3	chr1:175111400-175122600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:175111600-175119600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:175115000-175125000	Weak transcription	Right Atrium	heart
6	chr1:175115800-175120000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:175116000-175119200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr1:175116200-175119000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:175116200-175120000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:175116400-175119000	Weak transcription	Liver	Liver
11	chr1:175116400-175119200	Weak transcription	Fetal Heart	heart
12	chr1:175116400-175119400	Weak transcription	HMEC	breast
13	chr1:175116400-175121200	Weak transcription	Placenta	Placenta
14	chr1:175116600-175121400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:175116800-175121000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:175117600-175119200	Weak transcription	Fetal Brain Male	brain

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