Variant report

Variant	rs56197478
Chromosome Location	chr10:50301892-50301893
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10508911	0.96[EUR][1000 genomes]
rs10857434	0.93[EUR][1000 genomes]
rs11100985	0.95[EUR][1000 genomes]
rs11100994	0.91[EUR][1000 genomes]
rs11814668	0.91[EUR][1000 genomes]
rs11815070	0.91[EUR][1000 genomes]
rs12780892	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17011692	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17011715	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17011726	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17011755	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011799	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17773666	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28505677	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36116147	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4264085	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4272720	0.92[EUR][1000 genomes]
rs4453139	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs45563932	0.84[EUR][1000 genomes]
rs55648711	0.91[EUR][1000 genomes]
rs55872223	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55936311	0.91[EUR][1000 genomes]
rs56027486	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56157539	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59889308	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61166027	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61848370	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61848371	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61848377	0.96[EUR][1000 genomes]
rs61848380	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61850681	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61850682	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61850684	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61850689	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61850690	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61850693	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7084861	0.88[EUR][1000 genomes]
rs72785044	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72785050	0.91[EUR][1000 genomes]
rs72785051	0.91[EUR][1000 genomes]
rs72785060	0.92[EUR][1000 genomes]
rs72785072	0.90[EUR][1000 genomes]
rs72785076	0.91[EUR][1000 genomes]
rs72785084	0.89[EUR][1000 genomes]
rs72785087	0.89[EUR][1000 genomes]
rs72786903	0.82[EUR][1000 genomes]
rs72789086	0.81[EUR][1000 genomes]
rs7905715	0.81[EUR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56197478	C10orf128	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50290800-50315400	Weak transcription	Fetal Intestine Small	intestine
2	chr10:50292200-50302600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr10:50292200-50311800	Weak transcription	Aorta	Aorta
4	chr10:50293400-50312400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr10:50294800-50302600	Weak transcription	Brain Angular Gyrus	brain
6	chr10:50295800-50311600	Weak transcription	K562	blood
7	chr10:50296400-50302200	Enhancers	Right Ventricle	heart
8	chr10:50296400-50304000	Genic enhancers	Fetal Muscle Leg	muscle
9	chr10:50297600-50302800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr10:50297600-50303800	Genic enhancers	Fetal Muscle Trunk	muscle
11	chr10:50298400-50302400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr10:50298600-50302200	Weak transcription	Brain Substantia Nigra	brain
13	chr10:50298600-50302400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr10:50298600-50306000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr10:50298600-50306600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr10:50298600-50310400	Weak transcription	Fetal Intestine Large	intestine
17	chr10:50298600-50314400	Weak transcription	NHDF-Ad	bronchial
18	chr10:50298800-50302600	Weak transcription	Brain Hippocampus Middle	brain
19	chr10:50298800-50304200	Weak transcription	Fetal Heart	heart
20	chr10:50299000-50302200	Weak transcription	NHLF	lung
21	chr10:50299000-50312600	Weak transcription	Fetal Lung	lung
22	chr10:50299200-50303000	Weak transcription	Esophagus	oesophagus
23	chr10:50299200-50303200	Weak transcription	Psoas Muscle	Psoas
24	chr10:50299200-50307600	Weak transcription	Pancreas	Pancrea
25	chr10:50299400-50303600	Weak transcription	Lung	lung
26	chr10:50299600-50307400	Strong transcription	Fetal Stomach	stomach
27	chr10:50299600-50312200	Weak transcription	Colon Smooth Muscle	Colon
28	chr10:50299600-50314400	Weak transcription	HSMMtube	muscle
29	chr10:50300200-50302200	Weak transcription	Right Atrium	heart
30	chr10:50300200-50302400	Weak transcription	Adipose Nuclei	Adipose
31	chr10:50300800-50312400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr10:50300800-50314600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr10:50301000-50302000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr10:50301000-50302200	Weak transcription	Left Ventricle	heart
35	chr10:50301000-50302400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr10:50301000-50302400	Weak transcription	Ovary	ovary
37	chr10:50301600-50305400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr10:50301800-50302600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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