Variant report

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

rs_ID	r²[population]
rs11117765	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12031786	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4539203	1.00[ASW][hapmap]
rs4846808	0.90[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4846809	0.89[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4846810	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs924652	0.91[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs950482	0.91[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428610	chr1:217143317-217307243	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv549205	chr1:217165548-217270219	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4846812	RD3	cis	cerebellum	SCAN
rs4846812	USH2A	cis	parietal	SCAN
rs4846812	C1orf227	cis	parietal	SCAN
rs4846812	TMEM206	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:217221800-217251400	Weak transcription	Left Ventricle	heart
2	chr1:217223200-217250000	Weak transcription	Psoas Muscle	Psoas
3	chr1:217247800-217250600	Enhancers	Fetal Heart	heart
4	chr1:217248600-217251800	Enhancers	Fetal Stomach	stomach
5	chr1:217249400-217249600	Enhancers	Brain Hippocampus Middle	brain
6	chr1:217249400-217249600	Enhancers	Brain Substantia Nigra	brain
7	chr1:217249400-217249600	Enhancers	Colon Smooth Muscle	Colon
8	chr1:217249400-217249600	Enhancers	Fetal Brain Male	brain
9	chr1:217249400-217249600	Enhancers	Fetal Muscle Leg	muscle
10	chr1:217249400-217249600	Enhancers	Gastric	stomach
11	chr1:217249400-217249800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:217249400-217249800	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr1:217249400-217250000	Enhancers	Fetal Kidney	kidney
14	chr1:217249400-217250000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr1:217249400-217250400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:217249400-217250400	Active TSS	Pancreas	Pancrea
17	chr1:217249400-217250400	Enhancers	Rectal Smooth Muscle	rectum
18	chr1:217249400-217250600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr1:217249400-217251600	Active TSS	Brain Anterior Caudate	brain
20	chr1:217249400-217252400	Active TSS	Stomach Smooth Muscle	stomach

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