Variant report

Variant	rs2869030
Chromosome Location	chr15:78711803-78711804
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10519198	0.85[JPT][hapmap]
rs11639224	0.85[JPT][hapmap]
rs12899131	0.90[JPT][hapmap]
rs12909921	0.85[JPT][hapmap]
rs1847529	0.85[JPT][hapmap]
rs2869046	0.90[JPT][hapmap]
rs4436747	0.95[JPT][hapmap]
rs8041628	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
3	nsv833063	chr15:78605215-78754945	Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1627	chr15:78683761-78728604	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2869030	PSMA4	cis	cerebellum	SCAN
rs2869030	STOML1	cis	parietal	SCAN
rs2869030	PML	cis	parietal	SCAN
rs2869030	COX5A	cis	parietal	SCAN
rs2869030	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs2869030	PSMA4	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78698200-78729800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:78700800-78722000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:78706400-78712400	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr15:78707000-78712200	Enhancers	Fetal Intestine Small	intestine
5	chr15:78707200-78712600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr15:78709800-78715000	Enhancers	HepG2	liver
7	chr15:78710800-78714200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:78710800-78714600	Weak transcription	Colonic Mucosa	Colon
9	chr15:78710800-78715000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr15:78711200-78712600	Enhancers	Hela-S3	cervix
11	chr15:78711200-78713600	Enhancers	Placenta	Placenta
12	chr15:78711400-78712000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
13	chr15:78711600-78712000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:78711600-78715000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr15:78711800-78714000	Weak transcription	Fetal Intestine Large	intestine
16	chr15:78711800-78714600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr15:78711800-78715000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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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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