Variant report

Variant	rs56157539
Chromosome Location	chr10:50261880-50261881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:50242711..50245111-chr10:50261545..50265168,4	MCF-7	breast:
2	chr10:50261106..50262953-chr10:50265255..50267804,2	MCF-7	breast:
3	chr10:50255638..50257367-chr10:50260546..50263382,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10508911	0.90[EUR][1000 genomes]
rs10857434	0.88[EUR][1000 genomes]
rs11100985	0.90[EUR][1000 genomes]
rs11100994	0.85[EUR][1000 genomes]
rs11814668	0.85[EUR][1000 genomes]
rs11815070	0.85[EUR][1000 genomes]
rs12780892	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17011692	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17011715	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011726	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011755	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17011799	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17773666	0.93[EUR][1000 genomes]
rs28505677	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36116147	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4264085	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4272720	0.98[EUR][1000 genomes]
rs4453139	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55648711	0.85[EUR][1000 genomes]
rs55872223	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55936311	0.85[EUR][1000 genomes]
rs56027486	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56197478	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59889308	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61166027	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61848370	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61848371	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61848377	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61848380	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61850678	0.82[EUR][1000 genomes]
rs61850681	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61850682	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61850684	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61850689	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61850690	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61850693	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7084861	0.83[EUR][1000 genomes]
rs72785044	0.93[EUR][1000 genomes]
rs72785050	0.86[EUR][1000 genomes]
rs72785051	0.86[EUR][1000 genomes]
rs72785060	0.87[EUR][1000 genomes]
rs72785072	0.85[EUR][1000 genomes]
rs72785076	0.85[EUR][1000 genomes]
rs72785084	0.84[EUR][1000 genomes]
rs72785087	0.84[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
rs56157539	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	chr10:50232400-50279200	Weak transcription	Brain Hippocampus Middle	brain
3	chr10:50233000-50266000	Weak transcription	Colon Smooth Muscle	Colon
4	chr10:50241600-50263200	Weak transcription	NHLF	lung
5	chr10:50243800-50278800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr10:50245600-50264200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr10:50247000-50282600	Weak transcription	Brain Angular Gyrus	brain
8	chr10:50247800-50271600	Weak transcription	Fetal Intestine Small	intestine
9	chr10:50254400-50278800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr10:50255800-50270200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr10:50257200-50266800	Weak transcription	Aorta	Aorta
12	chr10:50258200-50265800	Weak transcription	Fetal Kidney	kidney
13	chr10:50259000-50262200	Weak transcription	Adipose Nuclei	Adipose
14	chr10:50259200-50264400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr10:50259400-50263000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr10:50259400-50263000	Weak transcription	NHDF-Ad	bronchial
17	chr10:50259800-50264000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr10:50260600-50262000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr10:50260600-50262400	Enhancers	GM12878-XiMat	blood
20	chr10:50260600-50267800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr10:50260800-50263200	Enhancers	Stomach Smooth Muscle	stomach
22	chr10:50261000-50262000	Enhancers	Fetal Muscle Leg	muscle
23	chr10:50261000-50262000	Enhancers	HSMM	muscle
24	chr10:50261200-50262600	Enhancers	Esophagus	oesophagus
25	chr10:50261200-50262600	Enhancers	Lung	lung
26	chr10:50261200-50263000	Genic enhancers	Fetal Muscle Trunk	muscle
27	chr10:50261200-50263600	Enhancers	Psoas Muscle	Psoas
28	chr10:50261200-50264800	Genic enhancers	Fetal Stomach	stomach
29	chr10:50261200-50265000	Enhancers	Right Atrium	heart
30	chr10:50261200-50267400	Enhancers	Right Ventricle	heart
31	chr10:50261200-50267600	Enhancers	Left Ventricle	heart
32	chr10:50261200-50267600	Enhancers	Ovary	ovary
33	chr10:50261400-50263200	Enhancers	Spleen	Spleen
34	chr10:50261400-50264200	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr10:50261600-50262600	Enhancers	HSMMtube	muscle
36	chr10:50261600-50263800	Enhancers	Fetal Lung	lung
37	chr10:50261800-50264600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr10:50261800-50264600	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links