Variant report

Variant	rs6869646
Chromosome Location	chr5:124470372-124470373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10036304	0.84[ASN][1000 genomes]
rs10040497	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10050592	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10050742	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10051335	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10067150	0.83[ASN][1000 genomes]
rs10067228	0.83[ASN][1000 genomes]
rs10068672	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10085148	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1008776	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1109910	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1109911	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1109912	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11241788	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241789	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11741331	0.84[EUR][1000 genomes]
rs11743350	0.83[ASN][1000 genomes]
rs11744843	0.83[ASN][1000 genomes]
rs11746972	0.83[ASN][1000 genomes]
rs11747137	0.83[ASN][1000 genomes]
rs12188105	0.87[ASN][1000 genomes]
rs12189383	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12520570	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13161894	0.80[ASN][1000 genomes]
rs13162105	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13162223	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13178008	0.87[ASN][1000 genomes]
rs13187207	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13188430	0.87[ASN][1000 genomes]
rs13359280	0.83[ASN][1000 genomes]
rs1371373	0.83[ASN][1000 genomes]
rs1371374	0.83[ASN][1000 genomes]
rs1550356	0.87[ASN][1000 genomes]
rs1550357	0.87[ASN][1000 genomes]
rs1550358	0.87[ASN][1000 genomes]
rs1550361	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1550364	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1550365	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17449514	0.87[ASN][1000 genomes]
rs17456443	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17456490	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17515092	0.84[ASN][1000 genomes]
rs2033842	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2218125	0.91[ASN][1000 genomes]
rs28662294	0.87[ASN][1000 genomes]
rs34348381	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34519250	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35918516	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4590178	0.84[ASN][1000 genomes]
rs4836151	0.87[ASN][1000 genomes]
rs4836153	0.87[ASN][1000 genomes]
rs4836155	0.87[ASN][1000 genomes]
rs5016080	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5016082	0.83[ASN][1000 genomes]
rs5016083	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56065010	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56171860	0.91[ASN][1000 genomes]
rs61581106	0.83[ASN][1000 genomes]
rs62375663	0.83[ASN][1000 genomes]
rs62375664	0.83[ASN][1000 genomes]
rs6595576	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6595577	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6595578	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6862170	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6865099	0.91[ASN][1000 genomes]
rs6865632	0.91[ASN][1000 genomes]
rs6885185	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6886317	0.91[ASN][1000 genomes]
rs6888003	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6892666	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6895171	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7719958	0.83[ASN][1000 genomes]
rs7720525	0.83[ASN][1000 genomes]
rs7721241	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7724689	0.83[ASN][1000 genomes]
rs7733868	0.91[ASN][1000 genomes]
rs7735615	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs893714	0.83[ASN][1000 genomes]
rs893715	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs893716	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs953844	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9686650	0.91[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	nsv830475	chr5:124387292-124550256	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv599658	chr5:124459547-124513012	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6869646	SNCAIP	cis	parietal	SCAN
rs6869646	FBXO36	trans	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:124465400-124471000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:124468200-124472000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr5:124469400-124472400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:124469800-124470600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:124469800-124471000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:124469800-124471000	Enhancers	Osteobl	bone
7	chr5:124469800-124471400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr5:124469800-124471400	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr5:124469800-124471400	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr5:124469800-124471400	Enhancers	Muscle Satellite Cultured Cells	--
11	chr5:124469800-124471400	Enhancers	HSMMtube	muscle
12	chr5:124470000-124470400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:124470000-124470600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:124470000-124470800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:124470000-124470800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:124470000-124470800	Enhancers	HUVEC	blood vessel
17	chr5:124470000-124470800	Enhancers	NHEK	skin
18	chr5:124470000-124471000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr5:124470000-124471000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:124470000-124471000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr5:124470000-124471000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:124470000-124471000	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr5:124470000-124471000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:124470000-124471000	Enhancers	Brain Anterior Caudate	brain
25	chr5:124470000-124471000	Enhancers	Brain Substantia Nigra	brain
26	chr5:124470000-124471000	Enhancers	NHDF-Ad	bronchial
27	chr5:124470000-124471200	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr5:124470000-124471400	Enhancers	HMEC	breast
29	chr5:124470000-124471400	Enhancers	NH-A	brain
30	chr5:124470000-124471600	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr5:124470000-124472000	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr5:124470200-124470800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr5:124470200-124471000	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr5:124470200-124471400	Enhancers	HSMM	muscle

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