Variant report

Variant	rs10885054
Chromosome Location	chr10:112588355-112588356
allele	A/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	chr10:112579505..112583802-chr10:112587400..112591373,5	MCF-7	breast:
3	chr10:112587964..112590825-chr10:112590840..112592788,2	K562	blood:
4	chr10:112582382..112584643-chr10:112585377..112589388,5	MCF-7	breast:
5	chr10:112580755..112589346-chr10:112627817..112636075,27	MCF-7	breast:

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

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10736209	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10787283	0.81[CEU][hapmap]
rs10885052	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10885053	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10885055	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1923807	0.80[AMR][1000 genomes]
rs1980689	0.83[CEU][hapmap]
rs2031128	0.90[JPT][hapmap]
rs3950000	0.81[ASN][1000 genomes]
rs4918595	0.86[AMR][1000 genomes]
rs4918598	0.85[JPT][hapmap]
rs4918599	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs4918600	0.85[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes]
rs4918601	1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7072681	0.85[CEU][hapmap];0.84[MEX][hapmap]
rs726803	0.82[CEU][hapmap];0.84[AMR][1000 genomes]
rs726804	0.81[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs7922732	0.95[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs942076	0.91[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10885054	PDCD4	Cis_1M	lymphoblastoid	RTeQTL
rs10885054	TECTB	cis	parietal	SCAN

Chromatin state (count:62 , 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	chr10:112578800-112592400	Weak transcription	Primary T cells from cord blood	blood
5	chr10:112580400-112589800	Enhancers	Colon Smooth Muscle	Colon
6	chr10:112582600-112593000	Weak transcription	K562	blood
7	chr10:112582600-112593400	Weak transcription	Gastric	stomach
8	chr10:112583200-112593400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr10:112583400-112588800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr10:112583400-112589200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr10:112583400-112590000	Enhancers	Rectal Smooth Muscle	rectum
12	chr10:112583400-112593800	Weak transcription	Fetal Kidney	kidney
13	chr10:112583400-112594400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr10:112583400-112594800	Weak transcription	Fetal Brain Female	brain
15	chr10:112584000-112589400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr10:112584400-112592400	Weak transcription	Stomach Mucosa	stomach
17	chr10:112584600-112594000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr10:112584600-112594000	Weak transcription	Small Intestine	intestine
19	chr10:112585400-112589000	Weak transcription	Left Ventricle	heart
20	chr10:112585600-112593800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr10:112585600-112594200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr10:112585800-112589400	Weak transcription	Fetal Intestine Small	intestine
23	chr10:112586400-112588400	Enhancers	Fetal Muscle Trunk	muscle
24	chr10:112586800-112588400	Enhancers	Fetal Muscle Leg	muscle
25	chr10:112586800-112588600	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr10:112586800-112588600	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr10:112586800-112589800	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr10:112586800-112590600	Enhancers	Fetal Stomach	stomach
29	chr10:112587000-112588400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr10:112587000-112588600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr10:112587000-112588600	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr10:112587200-112589000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr10:112587200-112589600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr10:112587200-112590200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr10:112587400-112588400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr10:112587400-112588400	Enhancers	Fetal Lung	lung
37	chr10:112587400-112588600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr10:112587400-112588600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr10:112587600-112588400	Enhancers	Aorta	Aorta
40	chr10:112587600-112588400	Enhancers	Right Atrium	heart
41	chr10:112587600-112588400	Enhancers	HMEC	breast
42	chr10:112587600-112588600	Enhancers	Ovary	ovary
43	chr10:112587600-112588800	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr10:112587600-112589200	Genic enhancers	Right Ventricle	heart
45	chr10:112587600-112591200	Enhancers	Esophagus	oesophagus
46	chr10:112587800-112588400	Enhancers	Brain Hippocampus Middle	brain
47	chr10:112587800-112588400	Enhancers	NHEK	skin
48	chr10:112587800-112592600	Weak transcription	Lung	lung
49	chr10:112587800-112593400	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr10:112588000-112588800	Weak transcription	Fetal Heart	heart

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