Variant report

Variant	rs1344352
Chromosome Location	chr9:98542410-98542411
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	chr9:98540410..98542743-chr9:98568688..98571195,2	MCF-7	breast:
2	chr9:98540353..98542848-chr9:98564326..98568031,3	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10817721	0.87[JPT][hapmap]
rs12347549	0.86[CHD][hapmap];0.80[MEX][hapmap]
rs1836406	0.84[MKK][hapmap]
rs4743306	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743316	0.86[CHB][hapmap]
rs6478964	0.86[CHB][hapmap]
rs7029459	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7045635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1344352	SLC35D2	cis	parietal	SCAN
rs1344352	FBP1	cis	parietal	SCAN

Chromatin state (count:21 , 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	chr9:98538600-98543800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:98540800-98542600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:98541200-98542600	Enhancers	Ovary	ovary
7	chr9:98541400-98543200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:98541400-98545800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:98541600-98543000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:98541600-98545000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr9:98541800-98543200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr9:98541800-98545800	Weak transcription	HSMMtube	muscle
13	chr9:98541800-98545800	Weak transcription	NHLF	lung
14	chr9:98542000-98543600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr9:98542000-98544800	Weak transcription	HepG2	liver
16	chr9:98542000-98545000	Weak transcription	HSMM	muscle
17	chr9:98542000-98545200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr9:98542000-98545800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:98542200-98543400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:98542400-98542600	Enhancers	Left Ventricle	heart
21	chr9:98542400-98543400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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