Variant report

Variant	rs4743320
Chromosome Location	chr9:98541215-98541216
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98539544..98541347-chr9:98636439..98639024,2	MCF-7	breast:
2	chr9:98540410..98542743-chr9:98568688..98571195,2	MCF-7	breast:
3	chr9:98540353..98542848-chr9:98564326..98568031,3	MCF-7	breast:
4	chr9:98530888..98533284-chr9:98539147..98541445,2	K562	blood:

Variant related genes	Relation type
ENSG00000175611	Chromatin interaction
ENSG00000182150	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10124062	0.83[AMR][1000 genomes]
rs28454319	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3739752	0.81[MEX][hapmap];0.81[AMR][1000 genomes]
rs4742751	1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs6478970	0.87[EUR][1000 genomes]
rs7042092	1.00[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7854146	0.94[CEU][hapmap];0.96[GIH][hapmap];0.93[MEX][hapmap];0.87[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	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4743320	BARX1	cis	parietal	SCAN
rs4743320	TBC1D2	cis	parietal	SCAN
rs4743320	ZNF484	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98535400-98550800	Weak transcription	Right Atrium	heart
2	chr9:98535600-98545800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:98536000-98546800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:98536400-98541400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr9:98538000-98541800	Enhancers	NHLF	lung
6	chr9:98538600-98543800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr9:98539400-98542000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr9:98539400-98542000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:98540000-98542400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:98540600-98541400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:98540800-98541400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:98540800-98541400	Enhancers	Fetal Muscle Trunk	muscle
13	chr9:98540800-98542000	Enhancers	HSMM	muscle
14	chr9:98540800-98542600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr9:98541000-98541600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:98541000-98541600	Enhancers	Fetal Lung	lung
17	chr9:98541000-98541600	Enhancers	Osteobl	bone
18	chr9:98541000-98541800	Enhancers	HSMMtube	muscle
19	chr9:98541000-98541800	Enhancers	NHDF-Ad	bronchial
20	chr9:98541000-98542000	Enhancers	Muscle Satellite Cultured Cells	--
21	chr9:98541000-98542000	Enhancers	HepG2	liver
22	chr9:98541200-98541600	Enhancers	Stomach Smooth Muscle	stomach
23	chr9:98541200-98541800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr9:98541200-98542000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr9:98541200-98542000	Enhancers	Fetal Muscle Leg	muscle
26	chr9:98541200-98542000	Enhancers	Fetal Stomach	stomach
27	chr9:98541200-98542600	Enhancers	Ovary	ovary

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