Variant report

Variant	rs4558089
Chromosome Location	chr10:50309330-50309331
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:50308627..50310723-chr10:50311028..50313744,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11100984	0.93[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12245255	0.84[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12246766	0.97[ASN][1000 genomes]
rs12255055	0.82[GIH][hapmap]
rs12777282	0.82[CHB][hapmap]
rs13088	1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs4240498	0.85[MEX][hapmap]
rs4240499	0.88[ASN][1000 genomes]
rs4265516	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4298825	0.92[CHB][hapmap];1.00[CHD][hapmap]
rs4421675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4488117	0.92[CHB][hapmap];1.00[CHD][hapmap]
rs4509682	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs6537494	0.85[MEX][hapmap]
rs6537497	0.86[JPT][hapmap]
rs7069758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7074818	0.81[MEX][hapmap]
rs7079570	1.00[ASW][hapmap];0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];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:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831866	chr10:50165180-50335276	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	esv2761593	chr10:50276812-50336129	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4558089	SYT15	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50290800-50315400	Weak transcription	Fetal Intestine Small	intestine
2	chr10:50292200-50311800	Weak transcription	Aorta	Aorta
3	chr10:50293400-50312400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr10:50295800-50311600	Weak transcription	K562	blood
5	chr10:50298600-50310400	Weak transcription	Fetal Intestine Large	intestine
6	chr10:50298600-50314400	Weak transcription	NHDF-Ad	bronchial
7	chr10:50299000-50312600	Weak transcription	Fetal Lung	lung
8	chr10:50299600-50312200	Weak transcription	Colon Smooth Muscle	Colon
9	chr10:50299600-50314400	Weak transcription	HSMMtube	muscle
10	chr10:50300800-50312400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr10:50300800-50314600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr10:50303200-50310600	Weak transcription	Brain Hippocampus Middle	brain
13	chr10:50303200-50314600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr10:50303400-50313600	Weak transcription	Brain Substantia Nigra	brain
15	chr10:50303400-50314400	Weak transcription	Brain Anterior Caudate	brain
16	chr10:50303600-50314400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr10:50303600-50314400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr10:50303800-50314600	Weak transcription	Esophagus	oesophagus
19	chr10:50304000-50309600	Weak transcription	Adipose Nuclei	Adipose
20	chr10:50304000-50314400	Weak transcription	Brain Angular Gyrus	brain
21	chr10:50304600-50314400	Weak transcription	Liver	Liver
22	chr10:50304800-50317600	Weak transcription	Fetal Heart	heart
23	chr10:50305400-50314400	Weak transcription	NHLF	lung
24	chr10:50305800-50313600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr10:50306400-50311600	Weak transcription	Right Atrium	heart
26	chr10:50306400-50314600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr10:50307000-50312000	Weak transcription	Left Ventricle	heart
28	chr10:50307000-50312400	Weak transcription	Right Ventricle	heart
29	chr10:50307200-50311800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr10:50307400-50310200	Weak transcription	Fetal Stomach	stomach
31	chr10:50307400-50311600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr10:50307400-50311600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr10:50307400-50312400	Weak transcription	Ovary	ovary
34	chr10:50307400-50314200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr10:50307400-50314400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr10:50307800-50310400	Weak transcription	Fetal Muscle Leg	muscle

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