Variant report

Variant	rs9642175
Chromosome Location	chr7:83802951-83802952
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:10)

rs_ID	r²[population]
rs11979170	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539919	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1986177	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7782557	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7800664	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7800995	0.91[ASN][1000 genomes]
rs7805512	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929275	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9642174	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs996033	1.00[ASW][hapmap];0.88[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];0.82[TSI][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529344	chr7:83714286-84592857	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv888629	chr7:83722691-83896025	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1017884	chr7:83724138-83972995	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv538995	chr7:83724138-83972995	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv888630	chr7:83782839-83809111	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9642175	GNAI1	cis	cerebellum	SCAN
rs9642175	KIAA1324L	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:83777000-83803000	Weak transcription	NHLF	lung
2	chr7:83778000-83803000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:83785000-83803000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:83787400-83803000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr7:83787800-83804600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:83792200-83820600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr7:83792400-83803000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr7:83792400-83803000	Weak transcription	Fetal Lung	lung
9	chr7:83792400-83803000	Weak transcription	Fetal Stomach	stomach
10	chr7:83792400-83803400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:83792600-83803000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr7:83795600-83803000	Weak transcription	NHDF-Ad	bronchial
13	chr7:83796200-83803000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr7:83797400-83804600	Weak transcription	Colon Smooth Muscle	Colon
15	chr7:83797600-83803000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:83798800-83803000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr7:83800800-83803000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr7:83800800-83803000	Weak transcription	Fetal Brain Male	brain
19	chr7:83800800-83816600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr7:83801600-83805800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr7:83802000-83803000	Weak transcription	A549	lung
22	chr7:83802000-83807400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:83802600-83803600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr7:83802800-83803400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
25	chr7:83802800-83804600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell

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