Variant report

Variant	rs1562782
Chromosome Location	chr11:10342711-10342712
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:10323501..10326681-chr11:10342125..10345667,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254554	Chromatin interaction
ENSG00000148926	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10770106	0.81[CEU][hapmap]
rs12281432	1.00[ASW][hapmap]
rs13306112	0.85[CHD][hapmap]
rs1372811	0.84[CEU][hapmap]
rs1822292	0.85[CHD][hapmap]
rs1822293	1.00[ASW][hapmap];0.84[CEU][hapmap];0.85[CHD][hapmap]
rs2084600	0.88[AFR][1000 genomes]
rs2923096	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2923097	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2923099	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2957683	0.93[AFR][1000 genomes]
rs2957692	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2957694	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7124401	0.85[CHD][hapmap]
rs7925720	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7935934	0.85[CHD][hapmap]
rs7938491	0.83[CHD][hapmap]

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	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1562782	LYVE1	cis	parietal	SCAN
rs1562782	SYT9	cis	cerebellum	SCAN
rs1562782	OR10A5	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10330800-10344400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr11:10331400-10343800	Weak transcription	NHLF	lung
3	chr11:10331800-10344200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr11:10336400-10343400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr11:10336400-10344000	Weak transcription	Osteobl	bone
6	chr11:10336600-10343200	Weak transcription	Stomach Mucosa	stomach
7	chr11:10337800-10343400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr11:10338400-10346800	Enhancers	NHDF-Ad	bronchial
9	chr11:10338600-10343000	Enhancers	Stomach Smooth Muscle	stomach
10	chr11:10338800-10344000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:10338800-10344000	Weak transcription	HUVEC	blood vessel
12	chr11:10339000-10344000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr11:10339200-10342800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr11:10339200-10344000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr11:10339200-10344400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr11:10339400-10344400	Weak transcription	Fetal Kidney	kidney
17	chr11:10339600-10342800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:10339600-10343400	Weak transcription	Placenta	Placenta
19	chr11:10339600-10344000	Weak transcription	Brain Anterior Caudate	brain
20	chr11:10339600-10344000	Weak transcription	Brain Substantia Nigra	brain
21	chr11:10339600-10348800	Weak transcription	Brain Hippocampus Middle	brain
22	chr11:10340000-10344000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr11:10340200-10343400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr11:10340200-10344000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr11:10340200-10344000	Weak transcription	Right Atrium	heart
26	chr11:10340200-10344200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr11:10340200-10344200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr11:10340200-10344400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr11:10340200-10344400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr11:10340200-10347400	Weak transcription	Pancreas	Pancrea
31	chr11:10340400-10343400	Weak transcription	Fetal Intestine Large	intestine
32	chr11:10340400-10343400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr11:10340400-10343400	Weak transcription	HSMM	muscle
34	chr11:10340400-10344000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr11:10340400-10344000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr11:10340400-10344000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr11:10340400-10344000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr11:10340400-10344000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr11:10340400-10344000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:10340400-10344000	Weak transcription	Fetal Intestine Small	intestine
41	chr11:10340400-10344000	Weak transcription	Psoas Muscle	Psoas
42	chr11:10340400-10344000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr11:10340400-10344000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr11:10340400-10344000	Weak transcription	NHEK	skin
45	chr11:10340400-10344200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:10340400-10344200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr11:10340400-10350000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr11:10340600-10344000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr11:10340600-10344000	Weak transcription	Right Ventricle	heart
50	chr11:10340600-10344000	Weak transcription	Dnd41	blood

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