Variant report

Variant	rs1780748
Chromosome Location	chr1:79181290-79181291
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10493615	0.84[ASN][1000 genomes]
rs11162539	0.84[ASN][1000 genomes]
rs11162540	0.84[ASN][1000 genomes]
rs11162541	0.82[ASN][1000 genomes]
rs11162542	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162544	0.84[ASN][1000 genomes]
rs11587990	0.82[ASN][1000 genomes]
rs12403117	0.84[ASN][1000 genomes]
rs12409331	0.84[ASN][1000 genomes]
rs12409781	0.84[ASN][1000 genomes]
rs17395034	0.84[ASN][1000 genomes]
rs17395097	0.84[ASN][1000 genomes]
rs17399158	0.84[ASN][1000 genomes]
rs17399192	0.84[ASN][1000 genomes]
rs17400419	0.84[JPT][hapmap]
rs1887286	0.84[ASN][1000 genomes]
rs1926897	0.83[ASN][1000 genomes]
rs1926898	0.83[ASN][1000 genomes]
rs1926901	0.81[ASN][1000 genomes]
rs1926902	0.84[ASN][1000 genomes]
rs1926903	0.84[ASN][1000 genomes]
rs1926904	0.84[ASN][1000 genomes]
rs1926905	0.84[ASN][1000 genomes]
rs273250	0.84[JPT][hapmap]
rs58150654	0.84[ASN][1000 genomes]
rs58921479	0.84[ASN][1000 genomes]
rs58945140	0.84[ASN][1000 genomes]
rs58993850	0.84[ASN][1000 genomes]
rs60311076	0.84[ASN][1000 genomes]
rs61613596	0.84[ASN][1000 genomes]
rs61681700	0.84[ASN][1000 genomes]
rs61770023	0.84[ASN][1000 genomes]
rs61770024	0.84[ASN][1000 genomes]
rs6424785	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6424786	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv491784	chr1:79146141-79853482	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv871588	chr1:79164901-79214489	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1780748	USP33	cis	parietal	SCAN
rs1780748	FUBP1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79178400-79184800	Enhancers	Muscle Satellite Cultured Cells	--
2	chr1:79178400-79185000	Enhancers	Osteobl	bone
3	chr1:79179800-79183400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:79180000-79184600	Enhancers	NHDF-Ad	bronchial
5	chr1:79180200-79182400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:79180400-79181400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:79180400-79182000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:79180600-79181800	Enhancers	NHLF	lung
9	chr1:79180600-79182000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:79180600-79184800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:79180800-79181800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:79180800-79181800	Weak transcription	Brain Germinal Matrix	brain
13	chr1:79180800-79182800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:79180800-79182800	Enhancers	HSMMtube	muscle
15	chr1:79181000-79181400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:79181000-79181400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:79181000-79181400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:79181000-79181400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:79181000-79181400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:79181000-79181400	Enhancers	Aorta	Aorta
21	chr1:79181000-79181600	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr1:79181000-79181800	Enhancers	HSMM	muscle
23	chr1:79181000-79182000	Enhancers	NH-A	brain
24	chr1:79181200-79181400	Enhancers	HUVEC	blood vessel
25	chr1:79181200-79181600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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