Variant report

Variant	rs1403956
Chromosome Location	chr1:85933638-85933639
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:85932580-85933962	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr1:85933410-85933751	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr1:85933326-85933729	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
DDAH1	TF binding region

Extended variants
information (count: 5 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11161618	0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs12135333	0.83[CHB][hapmap]
rs1403953	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1403956	PKN2	cis	parietal	SCAN
rs1403956	SYDE2	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85931200-85941600	Weak transcription	Aorta	Aorta
2	chr1:85931200-85942200	Weak transcription	Esophagus	oesophagus
3	chr1:85931800-85938800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:85931800-85938800	Weak transcription	HSMMtube	muscle
5	chr1:85931800-85942400	Weak transcription	NHLF	lung
6	chr1:85931800-85956000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:85931800-85960000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:85932000-85936400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:85932000-85936400	Weak transcription	NH-A	brain
10	chr1:85932000-85937400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:85932000-85939400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:85932000-85961400	Weak transcription	Fetal Stomach	stomach
13	chr1:85932200-85934000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:85932200-85945400	Weak transcription	HUVEC	blood vessel
15	chr1:85932400-85936800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:85933000-85936400	Weak transcription	Osteobl	bone
17	chr1:85933000-85943200	Strong transcription	HSMM	muscle
18	chr1:85933400-85933800	Enhancers	H9 Cell Line	embryonic stem cell
19	chr1:85933400-85933800	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr1:85933400-85933800	Enhancers	NHDF-Ad	bronchial
21	chr1:85933600-85933800	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr1:85933600-85933800	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr1:85933600-85933800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
24	chr1:85933600-85933800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:85933600-85934000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:85933600-85939200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:85933600-85943400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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