Variant report

Variant	rs1989963
Chromosome Location	chr7:83864172-83864173
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10081337	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10085599	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1015629	0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10231889	0.92[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10260152	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10263842	0.92[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10265795	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11971807	0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11979170	0.89[JPT][hapmap]
rs12539919	0.84[JPT][hapmap]
rs1808204	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2018407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189444	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2214503	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2372167	0.84[ASN][1000 genomes]
rs4607535	0.92[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs471152	0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs471477	0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs488333	0.84[ASN][1000 genomes]
rs512896	0.82[AFR][1000 genomes]
rs514083	0.91[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs521401	0.91[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs537358	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs569493	0.84[ASN][1000 genomes]
rs584566	0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs600346	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs645226	0.84[ASN][1000 genomes]
rs671711	0.84[ASN][1000 genomes]
rs6946162	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6964607	0.92[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs727784	0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7787024	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7794860	0.86[AFR][1000 genomes]
rs7799452	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs811622	0.86[ASN][1000 genomes]
rs812780	0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9642175	0.84[JPT][hapmap]
rs996033	0.83[JPT][hapmap]

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	esv2754468	chr7:83851249-84166749	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1989963	GNAI1	cis	cerebellum	SCAN
rs1989963	C7orf23	cis	cerebellum	SCAN
rs1989963	KIAA1324L	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:83857600-83874000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:83861000-83865000	Weak transcription	NHEK	skin
3	chr7:83861000-83865200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr7:83861200-83865000	Weak transcription	HMEC	breast
5	chr7:83861200-83865200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:83861200-83865200	Weak transcription	NH-A	brain
7	chr7:83861200-83865200	Weak transcription	NHDF-Ad	bronchial
8	chr7:83861200-83867000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr7:83862000-83865000	Weak transcription	Osteobl	bone
10	chr7:83862200-83865600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr7:83862400-83865000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr7:83862400-83865000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr7:83862400-83865200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr7:83862400-83865200	Weak transcription	A549	lung
15	chr7:83862400-83865200	Weak transcription	NHLF	lung
16	chr7:83862400-83865400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr7:83862600-83865000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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