Variant report

Variant	rs10885053
Chromosome Location	chr10:112586950-112586951
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:112586696..112589138-chr10:112631404..112633158,2	K562	blood:
2	chr10:112582382..112584643-chr10:112585377..112589388,5	MCF-7	breast:
3	chr10:112581444..112587243-chr10:112629842..112633404,6	MCF-7	breast:
4	chr10:112580755..112589346-chr10:112627817..112636075,27	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150593	Chromatin interaction
ENSG00000203497	Chromatin interaction
ENSG00000232470	Chromatin interaction
ENSG00000203867	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10736209	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10787283	0.83[AMR][1000 genomes]
rs10885052	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10885054	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10885055	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11195340	0.82[AMR][1000 genomes]
rs1923807	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1980689	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4918595	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4918598	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4918599	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4918600	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4918601	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7072681	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs726803	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs726804	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7922732	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs942076	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045608	chr10:112524813-112677557	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1041758	chr10:112552897-112677557	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv467455	chr10:112579299-112612471	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv552172	chr10:112579299-112612471	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv896003	chr10:112579299-112631211	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv896002	chr10:112579299-112638028	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv1051566	chr10:112580049-112730573	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10885053	PDCD4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112572600-112593800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:112577200-112590800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:112577800-112593400	Weak transcription	Thymus	Thymus
4	chr10:112578800-112587400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr10:112578800-112592400	Weak transcription	Primary T cells from cord blood	blood
6	chr10:112580400-112587400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr10:112580400-112587600	Weak transcription	Liver	Liver
8	chr10:112580400-112589800	Enhancers	Colon Smooth Muscle	Colon
9	chr10:112580600-112587000	Weak transcription	Lung	lung
10	chr10:112582600-112587000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr10:112582600-112593000	Weak transcription	K562	blood
12	chr10:112582600-112593400	Weak transcription	Gastric	stomach
13	chr10:112582800-112587400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr10:112583000-112587600	Weak transcription	Adipose Nuclei	Adipose
15	chr10:112583000-112587600	Weak transcription	Esophagus	oesophagus
16	chr10:112583000-112587600	Weak transcription	Ovary	ovary
17	chr10:112583000-112587600	Weak transcription	Right Ventricle	heart
18	chr10:112583200-112587400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr10:112583200-112587600	Weak transcription	Pancreas	Pancrea
20	chr10:112583200-112587800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr10:112583200-112588000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr10:112583200-112588200	Weak transcription	Colonic Mucosa	Colon
23	chr10:112583200-112593400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr10:112583400-112587400	Weak transcription	Fetal Lung	lung
25	chr10:112583400-112587600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr10:112583400-112588800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr10:112583400-112589200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr10:112583400-112590000	Enhancers	Rectal Smooth Muscle	rectum
29	chr10:112583400-112593800	Weak transcription	Fetal Kidney	kidney
30	chr10:112583400-112594400	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr10:112583400-112594800	Weak transcription	Fetal Brain Female	brain
32	chr10:112583600-112587400	Weak transcription	Brain Anterior Caudate	brain
33	chr10:112583600-112587600	Weak transcription	Right Atrium	heart
34	chr10:112583800-112587200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr10:112584000-112589400	Weak transcription	Primary B cells from peripheral blood	blood
36	chr10:112584200-112587800	Weak transcription	Brain Hippocampus Middle	brain
37	chr10:112584200-112588200	Weak transcription	Fetal Thymus	thymus
38	chr10:112584400-112587600	Weak transcription	Aorta	Aorta
39	chr10:112584400-112587600	Weak transcription	Fetal Brain Male	brain
40	chr10:112584400-112592400	Weak transcription	Stomach Mucosa	stomach
41	chr10:112584600-112594000	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr10:112584600-112594000	Weak transcription	Small Intestine	intestine
43	chr10:112584800-112587200	Weak transcription	HSMMtube	muscle
44	chr10:112584800-112587600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr10:112584800-112587600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr10:112584800-112587600	Weak transcription	Psoas Muscle	Psoas
47	chr10:112585000-112587600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr10:112585000-112588000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr10:112585400-112589000	Weak transcription	Left Ventricle	heart
50	chr10:112585600-112587200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links