Variant report

Variant	rs4743316
Chromosome Location	chr9:98540112-98540113
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98539544..98541347-chr9:98636439..98639024,2	MCF-7	breast:
2	chr9:98530888..98533284-chr9:98539147..98541445,2	K562	blood:

Variant related genes	Relation type
ENSG00000182150	Chromatin interaction
ENSG00000175611	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1344352	0.86[CHB][hapmap]
rs4742753	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4743306	0.86[CHB][hapmap]
rs4743317	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478964	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6478965	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7029459	0.86[CHB][hapmap]
rs7035466	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7045260	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7045635	0.86[CHB][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	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
rs4743316	SLC35D2	cis	parietal	SCAN
rs4743316	BARX1	cis	parietal	SCAN
rs4743316	XPA	cis	parietal	SCAN

Chromatin state (count:23 , 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	chr9:98537400-98541000	Weak transcription	HepG2	liver
6	chr9:98537800-98541200	Weak transcription	Ovary	ovary
7	chr9:98538000-98541800	Enhancers	NHLF	lung
8	chr9:98538600-98543800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr9:98539000-98540400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:98539000-98541200	Weak transcription	Fetal Muscle Leg	muscle
11	chr9:98539200-98541000	Weak transcription	Fetal Lung	lung
12	chr9:98539200-98541000	Weak transcription	HSMMtube	muscle
13	chr9:98539200-98541000	Weak transcription	NHDF-Ad	bronchial
14	chr9:98539400-98541200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr9:98539400-98542000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:98539400-98542000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:98539800-98540200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:98539800-98541200	Weak transcription	Fetal Stomach	stomach
19	chr9:98540000-98540200	Weak transcription	Lung	lung
20	chr9:98540000-98540600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr9:98540000-98540800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr9:98540000-98541200	Weak transcription	Fetal Heart	heart
23	chr9:98540000-98542400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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