Variant report

Variant	rs3752534
Chromosome Location	chr6:164529381-164529382
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10945957	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs169580	0.90[JPT][hapmap]
rs206704	0.82[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs206705	0.91[JPT][hapmap]
rs206707	0.95[JPT][hapmap]
rs206708	0.91[JPT][hapmap]
rs3752533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018860	chr6:163939347-164532579	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538526	chr6:163939347-164532579	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1026707	chr6:164188210-164749206	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv538527	chr6:164188210-164749206	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1029952	chr6:164463355-165268911	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv1828570	chr6:164528407-164546547	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3752534	RP1-155D22.1	cis	Muscle Skeletal	GTEx
rs3752534	PLG	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:164506400-164530200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:164523200-164529400	Weak transcription	Right Atrium	heart
3	chr6:164523200-164530600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:164523400-164536400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:164524800-164531800	Enhancers	Fetal Muscle Leg	muscle
6	chr6:164527200-164530400	Enhancers	Fetal Muscle Trunk	muscle
7	chr6:164527200-164531600	Enhancers	Fetal Heart	heart
8	chr6:164527600-164529400	Weak transcription	Brain Anterior Caudate	brain
9	chr6:164527800-164529600	Enhancers	K562	blood
10	chr6:164528000-164529400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:164528000-164529400	Enhancers	HSMM	muscle
12	chr6:164528000-164529600	Weak transcription	Right Ventricle	heart
13	chr6:164528000-164529800	Weak transcription	Brain Hippocampus Middle	brain
14	chr6:164528000-164537200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:164528400-164529600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:164528400-164529600	Enhancers	Psoas Muscle	Psoas
17	chr6:164528400-164530200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:164528800-164529800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:164528800-164529800	Enhancers	Muscle Satellite Cultured Cells	--
20	chr6:164528800-164531000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:164529000-164530000	Enhancers	Left Ventricle	heart
22	chr6:164529000-164530200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:164529000-164530200	Enhancers	NH-A	brain
24	chr6:164529000-164531000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr6:164529200-164529400	Enhancers	Brain Substantia Nigra	brain
26	chr6:164529200-164529600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:164529200-164529600	Enhancers	Adipose Nuclei	Adipose
28	chr6:164529200-164529600	Enhancers	Liver	Liver
29	chr6:164529200-164529600	Weak transcription	Esophagus	oesophagus
30	chr6:164529200-164530200	Flanking Active TSS	HSMMtube	muscle
31	chr6:164529200-164530600	Enhancers	Spleen	Spleen
32	chr6:164529200-164531200	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr6:164529200-164531200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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