Variant report

Variant	rs1959088
Chromosome Location	chr14:56197878-56197879
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10129360	0.96[ASN][1000 genomes]
rs10148235	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10150277	0.93[ASN][1000 genomes]
rs12888097	0.90[JPT][hapmap]
rs17128741	0.93[ASN][1000 genomes]
rs17128756	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1953353	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1953354	0.94[ASN][1000 genomes]
rs1959087	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7145139	0.92[ASN][1000 genomes]
rs7145545	0.92[ASN][1000 genomes]
rs8015113	0.86[EUR][1000 genomes]
rs868199	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs868200	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs869661	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832804	chr14:56083850-56277632	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv901966	chr14:56160904-56436203	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv901967	chr14:56183127-56252062	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv901968	chr14:56183127-56256651	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv901969	chr14:56183127-56258997	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv901970	chr14:56183127-56265176	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv901971	chr14:56183127-56265176	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv901972	chr14:56185501-56256651	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv901973	chr14:56185908-56252062	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv901974	chr14:56192577-56252062	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv901975	chr14:56192577-56260033	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv901976	chr14:56192577-56265176	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1959088	KTN1	cis	cerebellum	SCAN
rs1959088	KTN1	cis	parietal	SCAN
rs1959088	FBXO34	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56191200-56206600	Weak transcription	Aorta	Aorta
2	chr14:56196400-56198600	Enhancers	A549	lung
3	chr14:56197000-56199200	Enhancers	Fetal Thymus	thymus
4	chr14:56197000-56201000	Enhancers	Hela-S3	cervix
5	chr14:56197200-56198000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr14:56197400-56198000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr14:56197400-56198600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr14:56197400-56198600	Enhancers	Brain Angular Gyrus	brain
9	chr14:56197400-56198600	Enhancers	Brain Hippocampus Middle	brain
10	chr14:56197400-56198600	Enhancers	Brain Substantia Nigra	brain
11	chr14:56197400-56198600	Enhancers	Fetal Brain Male	brain
12	chr14:56197400-56198600	Enhancers	Thymus	Thymus
13	chr14:56197400-56199600	Enhancers	Stomach Mucosa	stomach
14	chr14:56197600-56198200	Enhancers	Colon Smooth Muscle	Colon
15	chr14:56197600-56198600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr14:56197600-56198600	Enhancers	Brain Cingulate Gyrus	brain
17	chr14:56197600-56198600	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr14:56197800-56198200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr14:56197800-56198600	Enhancers	Duodenum Smooth Muscle	Duodenum

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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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