Variant report

Variant	rs2199395
Chromosome Location	chr14:25274297-25274298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12432022	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1461642	0.83[AMR][1000 genomes]
rs17200659	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17200666	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17795604	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1957760	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2199394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4983023	0.82[GIH][hapmap];0.92[MEX][hapmap];0.83[AMR][1000 genomes]
rs4983024	0.82[GIH][hapmap];0.92[MEX][hapmap];0.83[AMR][1000 genomes]
rs61976829	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61976831	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs725230	1.00[ASW][hapmap];0.86[GIH][hapmap];0.92[MEX][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8019575	0.82[GIH][hapmap];0.92[MEX][hapmap];0.83[AMR][1000 genomes]
rs965383	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv901504	chr14:25184210-25646203	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv901505	chr14:25237268-25360584	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1035284	chr14:25267840-25285191	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
6	nsv542003	chr14:25267840-25285191	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
7	nsv525203	chr14:25270335-25282967	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
8	nsv456169	chr14:25270335-25288227	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
9	nsv564071	chr14:25270335-25288227	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2199395	SLC7A8	cis	cerebellum	SCAN
rs2199395	RNASE7	cis	parietal	SCAN
rs2199395	METTL3	cis	parietal	SCAN
rs2199395	REM2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25272200-25275400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr14:25272400-25283400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr14:25273200-25276800	Enhancers	Placenta Amnion	Placenta Amnion
4	chr14:25273400-25274600	Enhancers	Lung	lung
5	chr14:25273400-25275200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr14:25273400-25276200	Enhancers	Fetal Lung	lung
7	chr14:25273400-25276200	Enhancers	HepG2	liver
8	chr14:25273400-25277600	Enhancers	Fetal Intestine Small	intestine
9	chr14:25273400-25277600	Weak transcription	Pancreas	Pancrea
10	chr14:25273400-25278200	Enhancers	Fetal Intestine Large	intestine
11	chr14:25273800-25276000	Enhancers	Stomach Mucosa	stomach
12	chr14:25274000-25274600	Enhancers	Duodenum Mucosa	Duodenum
13	chr14:25274000-25275400	Weak transcription	Right Ventricle	heart
14	chr14:25274000-25283000	Weak transcription	Gastric	stomach
15	chr14:25274200-25274600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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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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