Variant report

Variant	rs2527039
Chromosome Location	chr7:83689614-83689615
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1357813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189849	0.90[MEX][hapmap]
rs2189850	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2527030	0.80[EUR][1000 genomes]
rs2527031	0.85[MEX][hapmap]
rs2527032	0.90[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527040	0.92[JPT][hapmap];0.92[TSI][hapmap]
rs2691702	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906193	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4355720	0.80[MEX][hapmap];0.83[MKK][hapmap]
rs9690948	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv888624	chr7:83596683-83698177	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv888626	chr7:83651854-83698177	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv888627	chr7:83659577-83708238	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv888628	chr7:83659577-83722691	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2527039	SLC25A40	cis	parietal	SCAN
rs2527039	ZNF500	trans	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:83673800-83707600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr7:83678800-83690400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:83685800-83690200	Weak transcription	NHDF-Ad	bronchial
4	chr7:83685800-83690400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr7:83685800-83691600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr7:83685800-83691800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:83686000-83691600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr7:83687200-83691400	Enhancers	NHEK	skin
9	chr7:83687400-83691000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:83687400-83691200	Enhancers	HMEC	breast
11	chr7:83687600-83690200	Enhancers	HUVEC	blood vessel
12	chr7:83688000-83689800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:83688000-83689800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr7:83688400-83691400	Enhancers	Hela-S3	cervix
15	chr7:83688600-83689800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr7:83688600-83690000	Weak transcription	NHLF	lung
17	chr7:83688600-83690200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr7:83688600-83690200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:83688600-83690200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr7:83688600-83690200	Enhancers	NH-A	brain
21	chr7:83688800-83689800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr7:83688800-83689800	Enhancers	A549	lung
23	chr7:83688800-83690000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr7:83688800-83690000	Weak transcription	HepG2	liver
25	chr7:83688800-83690200	Weak transcription	Osteobl	bone
26	chr7:83688800-83690400	Weak transcription	Fetal Intestine Large	intestine
27	chr7:83689000-83691800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr7:83689200-83691400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr7:83689400-83690800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr7:83689600-83691200	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr7:83689600-83691600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr7:83689600-83697800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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