Variant report

Variant	rs12780892
Chromosome Location	chr10:50247010-50247011
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:50226547..50228210-chr10:50244930..50247229,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10508911	0.81[EUR][1000 genomes]
rs10857434	0.82[EUR][1000 genomes]
rs11100985	0.80[EUR][1000 genomes]
rs11816318	0.84[EUR][1000 genomes]
rs11817325	0.83[EUR][1000 genomes]
rs17011692	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17011715	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17011726	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17011755	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17011799	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17773666	0.82[EUR][1000 genomes]
rs2377692	0.83[EUR][1000 genomes]
rs28505677	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36116147	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4264085	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4272720	0.90[EUR][1000 genomes]
rs4453139	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55872223	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56027486	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56157539	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56197478	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59889308	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61166027	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61848153	0.83[EUR][1000 genomes]
rs61848370	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61848371	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61848377	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61848380	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61850678	0.86[EUR][1000 genomes]
rs61850681	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61850682	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61850684	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61850689	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61850690	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61850693	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72785044	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12780892	C10orf128	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50222800-50279000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr10:50223000-50254200	Weak transcription	NHDF-Ad	bronchial
3	chr10:50224400-50258200	Weak transcription	Brain Anterior Caudate	brain
4	chr10:50232400-50279200	Weak transcription	Brain Hippocampus Middle	brain
5	chr10:50232800-50247800	Weak transcription	Right Atrium	heart
6	chr10:50232800-50255400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr10:50233000-50266000	Weak transcription	Colon Smooth Muscle	Colon
8	chr10:50233800-50261400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr10:50233800-50261400	Weak transcription	Spleen	Spleen
10	chr10:50234000-50249000	Strong transcription	Fetal Muscle Leg	muscle
11	chr10:50234000-50254200	Weak transcription	Left Ventricle	heart
12	chr10:50237600-50248800	Weak transcription	Liver	Liver
13	chr10:50240600-50247200	Weak transcription	HSMMtube	muscle
14	chr10:50240600-50247400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr10:50241600-50263200	Weak transcription	NHLF	lung
16	chr10:50242400-50258000	Weak transcription	Fetal Kidney	kidney
17	chr10:50242400-50259200	Weak transcription	Brain Substantia Nigra	brain
18	chr10:50243200-50247200	Weak transcription	Esophagus	oesophagus
19	chr10:50243400-50261200	Weak transcription	Lung	lung
20	chr10:50243800-50278800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr10:50245400-50258200	Weak transcription	Osteobl	bone
22	chr10:50245600-50264200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr10:50245800-50247200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr10:50245800-50257800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr10:50246200-50247800	Strong transcription	Fetal Lung	lung
26	chr10:50246200-50248000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr10:50246400-50247200	Strong transcription	Adipose Nuclei	Adipose
28	chr10:50246600-50247800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr10:50246600-50247800	Strong transcription	Aorta	Aorta
30	chr10:50246600-50248200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr10:50246600-50248200	Strong transcription	Stomach Smooth Muscle	stomach
32	chr10:50246600-50248400	Strong transcription	Ovary	ovary
33	chr10:50246800-50247800	Strong transcription	Fetal Intestine Small	intestine
34	chr10:50246800-50248200	Genic enhancers	Fetal Muscle Trunk	muscle
35	chr10:50247000-50248000	Strong transcription	Right Ventricle	heart
36	chr10:50247000-50249000	Strong transcription	Fetal Stomach	stomach
37	chr10:50247000-50259000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr10:50247000-50282600	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links