Variant report

Variant	rs12889534
Chromosome Location	chr14:31709503-31709504
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10135901	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10137205	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11156659	0.87[EUR][1000 genomes]
rs12185024	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12883671	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12883762	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12893153	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12893469	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12895556	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12897427	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12898184	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2093616	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2378833	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4981829	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4981830	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs55633656	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7161558	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72672613	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8014203	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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	nsv901587	chr14:31501505-31752664	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1050054	chr14:31501703-31733642	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv2830427	chr14:31639110-32000034	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12889534	RP11-176H8.1	cis	Muscle Skeletal	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:31703000-31710200	Weak transcription	Fetal Heart	heart
2	chr14:31707800-31710600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr14:31707800-31710600	Weak transcription	Colon Smooth Muscle	Colon
4	chr14:31707800-31710600	Weak transcription	Stomach Mucosa	stomach
5	chr14:31707800-31711000	Weak transcription	Esophagus	oesophagus
6	chr14:31707800-31711000	Weak transcription	Spleen	Spleen
7	chr14:31707800-31712800	Weak transcription	Lung	lung
8	chr14:31707800-31713400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr14:31707800-31730800	Weak transcription	Pancreas	Pancrea
10	chr14:31708600-31710000	Enhancers	GM12878-XiMat	blood
11	chr14:31708800-31709800	Enhancers	HepG2	liver
12	chr14:31708800-31710600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr14:31709000-31710800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr14:31709000-31710800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr14:31709000-31713800	Enhancers	K562	blood
16	chr14:31709200-31710800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr14:31709400-31710800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr14:31709400-31710800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr14:31709400-31711000	Weak transcription	Small Intestine	intestine

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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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