Variant report

Variant	rs1739091
Chromosome Location	chr6:15081252-15081253
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1980528	0.84[AFR][1000 genomes]
rs2747507	1.00[ASW][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs2994318	0.84[AFR][1000 genomes]
rs4715959	0.80[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883454	chr6:15009137-15081252	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv830593	chr6:15049636-15244190	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1739091	PHACTR1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15077000-15090000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:15078400-15086600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:15078400-15086800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:15078600-15082600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:15078600-15083200	Enhancers	Fetal Intestine Large	intestine
6	chr6:15078600-15083800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr6:15078800-15087400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:15080000-15081600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:15080000-15089400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:15080200-15081600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:15080200-15083800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:15080200-15086600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:15080400-15081400	Weak transcription	Fetal Intestine Small	intestine
14	chr6:15080400-15086800	Weak transcription	Right Atrium	heart
15	chr6:15080800-15082000	Enhancers	Stomach Mucosa	stomach
16	chr6:15081200-15081400	Enhancers	H9 Cell Line	embryonic stem cell
17	chr6:15081200-15081400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr6:15081200-15081400	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr6:15081200-15082000	Flanking Active TSS	K562	blood

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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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