Variant report

Variant	rs56311153
Chromosome Location	chr4:122729685-122729686
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	chr4:122727884..122730425-chr4:122743286..122746200,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145386	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11098645	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098648	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731570	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731917	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12512876	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1396080	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1507994	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1507995	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17452156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2063165	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071486	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2221628	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3217753	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3217771	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3217773	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3217780	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828485	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3924987	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4077102	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4516739	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56077950	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56159666	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58649165	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61217486	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6534323	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67772833	0.95[EUR][1000 genomes]
rs6813653	0.81[ASN][1000 genomes]
rs6815790	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6821305	0.90[ASN][1000 genomes]
rs6823818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824258	0.80[ASN][1000 genomes]
rs6826506	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6838153	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6855269	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72680779	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7660548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686084	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686200	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7691955	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs769238	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs769246	0.92[EUR][1000 genomes]
rs7699776	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9684587	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817261	chr4:122085173-123020068	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv997539	chr4:122544104-123274266	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv530157	chr4:122557302-123248756	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56311153	EXOSC9	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122723000-122733400	Weak transcription	Pancreas	Pancrea
2	chr4:122723000-122743600	Weak transcription	Esophagus	oesophagus
3	chr4:122723000-122743600	Weak transcription	Small Intestine	intestine
4	chr4:122723000-122744200	Weak transcription	Gastric	stomach
5	chr4:122723000-122744600	Weak transcription	Aorta	Aorta
6	chr4:122723200-122731400	Weak transcription	Right Ventricle	heart
7	chr4:122723200-122737000	Weak transcription	Colonic Mucosa	Colon
8	chr4:122723200-122741800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:122723200-122743400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr4:122723200-122743600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:122723200-122743800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr4:122723400-122744200	Weak transcription	Stomach Mucosa	stomach
13	chr4:122723600-122732400	Weak transcription	Psoas Muscle	Psoas
14	chr4:122723600-122742200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:122723600-122742400	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr4:122723600-122742800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:122723800-122733000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:122723800-122734000	Strong transcription	Left Ventricle	heart
19	chr4:122723800-122736400	Strong transcription	Fetal Muscle Leg	muscle
20	chr4:122723800-122739400	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr4:122723800-122739600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr4:122723800-122739600	Strong transcription	Liver	Liver
23	chr4:122723800-122740000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr4:122723800-122740000	Strong transcription	Osteobl	bone
25	chr4:122723800-122740400	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr4:122723800-122740400	Strong transcription	Fetal Intestine Large	intestine
27	chr4:122723800-122740600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:122723800-122741800	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr4:122723800-122742200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:122723800-122742400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:122723800-122743000	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr4:122723800-122743000	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr4:122723800-122743000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr4:122724000-122730200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr4:122724000-122731600	Strong transcription	Brain Anterior Caudate	brain
36	chr4:122724000-122732400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:122724000-122733000	Strong transcription	Fetal Lung	lung
38	chr4:122724000-122735800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:122724000-122738200	Strong transcription	NHDF-Ad	bronchial
40	chr4:122724000-122740000	Strong transcription	Primary B cells from cord blood	blood
41	chr4:122724000-122740200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr4:122724000-122740400	Strong transcription	Placenta	Placenta
43	chr4:122724000-122740400	Strong transcription	NH-A	brain
44	chr4:122724000-122741800	Strong transcription	Fetal Muscle Trunk	muscle
45	chr4:122724000-122742600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr4:122724000-122743400	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr4:122724200-122736000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:122724200-122739000	Weak transcription	Fetal Heart	heart
49	chr4:122724200-122740200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:122724200-122740400	Strong transcription	Stomach Smooth Muscle	stomach

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