Variant report

Variant	rs7530143
Chromosome Location	chr1:79133391-79133392
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10493611	0.87[ASN][1000 genomes]
rs11577395	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12409167	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1547181	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3766325	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56216300	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59610674	0.90[ASN][1000 genomes]
rs6424781	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6669498	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6695058	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7514391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517942	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7523042	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7526598	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7526782	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7526927	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7533325	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7543088	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[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	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv830315	chr1:79008443-79200591	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv871140	chr1:79095581-79155134	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7530143	FGD6	trans	cerebellum	SCAN
rs7530143	IFI44	cis	parietal	SCAN
rs7530143	ATP13A1	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79117400-79144000	Weak transcription	Esophagus	oesophagus
2	chr1:79117400-79144000	Weak transcription	Spleen	Spleen
3	chr1:79117600-79153000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:79124800-79134000	Weak transcription	NHDF-Ad	bronchial
5	chr1:79126400-79138000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:79126600-79148000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr1:79129000-79138200	Weak transcription	Lung	lung
8	chr1:79129200-79143800	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:79129400-79133400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:79129400-79135800	Weak transcription	Left Ventricle	heart
11	chr1:79129400-79137600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:79129400-79138200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:79129400-79138200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:79129400-79138600	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:79129400-79139800	Weak transcription	Primary T cells from cord blood	blood
16	chr1:79129400-79144000	Weak transcription	Ovary	ovary
17	chr1:79129600-79141800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:79130000-79134200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:79130000-79141200	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:79130200-79133400	Weak transcription	Liver	Liver
21	chr1:79130200-79135200	Weak transcription	Dnd41	blood
22	chr1:79130200-79141800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:79130800-79135200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:79130800-79135600	Weak transcription	GM12878-XiMat	blood
25	chr1:79130800-79144000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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