Variant report

Variant	rs11253480
Chromosome Location	chr10:912826-912827
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:907666..909265-chr10:909779..913077,3	MCF-7	breast:
2	chr10:909518..913161-chr10:914478..916410,3	MCF-7	breast:
3	chr10:911717..913910-chr10:1101611..1103898,2	K562	blood:
4	chr10:912748..914379-chr10:915301..918260,2	K562	blood:

Variant related genes	Relation type
ENSG00000047056	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10752021	0.84[ASN][1000 genomes]
rs10904572	0.81[ASN][1000 genomes]
rs11253474	0.93[ASN][1000 genomes]
rs11253487	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2274375	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35913002	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3763722	0.80[ASN][1000 genomes]
rs4880743	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7079260	0.84[ASN][1000 genomes]
rs73584576	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs748112	0.81[ASN][1000 genomes]
rs752375	0.81[ASN][1000 genomes]
rs9124	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916591	chr10:224406-1088734	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv540386	chr10:224406-1197416	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1054659	chr10:611444-1133578	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
4	nsv948602	chr10:708293-944641	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv949063	chr10:708293-974870	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv466697	chr10:734229-1129527	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
7	nsv549765	chr10:734229-1129527	Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1043812	chr10:776547-981126	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv540406	chr10:776547-981126	Bivalent Enhancer Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv530116	chr10:776548-1401075	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
11	nsv948978	chr10:813426-1019115	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1048707	chr10:834439-915534	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
13	nsv1052540	chr10:887562-1300134	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
14	nsv540407	chr10:887562-1300134	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11253480	LARP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:852200-956400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:870600-959400	Weak transcription	Stomach Mucosa	stomach
3	chr10:883200-917200	Weak transcription	Colonic Mucosa	Colon
4	chr10:886800-924400	Weak transcription	Fetal Brain Male	brain
5	chr10:890400-916000	Weak transcription	Aorta	Aorta
6	chr10:897200-929600	Strong transcription	Primary T cells from cord blood	blood
7	chr10:899000-932000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr10:899200-913000	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr10:899200-913000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr10:899400-920200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr10:899800-931200	Strong transcription	Primary B cells from cord blood	blood
12	chr10:901000-914400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr10:901000-932000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr10:902000-913200	Strong transcription	Fetal Intestine Large	intestine
15	chr10:902000-933200	Strong transcription	Dnd41	blood
16	chr10:903000-915000	Strong transcription	Primary B cells from peripheral blood	blood
17	chr10:903200-922600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr10:903200-931800	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr10:903600-913000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr10:903600-931800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr10:904600-913200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr10:904800-913000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr10:904800-913200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr10:905000-913200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr10:905000-913200	Strong transcription	HSMM	muscle
26	chr10:905000-931600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr10:905200-913200	Strong transcription	Liver	Liver
28	chr10:905200-915000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr10:905200-931600	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr10:905400-913200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr10:905400-913400	Strong transcription	Placenta	Placenta
32	chr10:905400-918800	Strong transcription	Primary hematopoietic stem cells	blood
33	chr10:905400-919000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr10:905400-919000	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr10:905600-913200	Strong transcription	Duodenum Mucosa	Duodenum
36	chr10:905800-913000	Strong transcription	Osteobl	bone
37	chr10:905800-913200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr10:906000-913200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr10:906200-913000	Strong transcription	HepG2	liver
40	chr10:906600-913800	Strong transcription	Fetal Intestine Small	intestine
41	chr10:906600-913800	Strong transcription	Fetal Stomach	stomach
42	chr10:907600-923600	Weak transcription	Fetal Kidney	kidney
43	chr10:908000-927200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr10:908200-932600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr10:909000-913200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr10:909000-917400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr10:909000-917800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr10:909200-916200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr10:909200-923400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr10:909400-913200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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