Variant report

Variant	rs58553067
Chromosome Location	chr14:69822927-69822928
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:69808456..69811857-chr14:69822855..69826097,4	MCF-7	breast:
2	chr14:69821172..69826934-chr14:69835934..69842143,9	MCF-7	breast:
3	chr14:69720076..69722559-chr14:69822737..69824435,2	MCF-7	breast:
4	chr14:69810681..69813205-chr14:69822055..69824419,2	K562	blood:
5	chr14:69822349..69827857-chr14:69829114..69832930,7	MCF-7	breast:
6	chr14:69618455..69620714-chr14:69822372..69824189,2	MCF-7	breast:
7	chr14:69822116..69824651-chr14:69862569..69864900,2	MCF-7	breast:
8	chr14:69713333..69716497-chr14:69822464..69825610,4	MCF-7	breast:
9	chr14:69821722..69824231-chr14:69923203..69925103,2	MCF-7	breast:
10	chr14:69785427..69787621-chr14:69822775..69825192,2	MCF-7	breast:
11	chr14:69800242..69802795-chr14:69820027..69823716,5	MCF-7	breast:
12	chr14:69818637..69821416-chr14:69822734..69824563,2	K562	blood:
13	chr14:69821220..69824181-chr14:69864124..69866738,3	MCF-7	breast:
14	chr14:69811705..69814388-chr14:69822919..69825901,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000029364	Chromatin interaction
ENSG00000100626	Chromatin interaction
ENSG00000100632	Chromatin interaction
ENSG00000139990	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10083335	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10129186	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10138313	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10140273	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10142144	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10143593	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11622711	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11624577	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12878175	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12884348	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12884802	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12893282	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12895620	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1958121	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2085193	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2124191	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2296722	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2296724	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2296725	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2296727	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28401542	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28451089	0.81[AMR][1000 genomes]
rs28470369	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28661733	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34450502	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34731892	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34834622	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34840252	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3759771	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4899294	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4899295	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4902717	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56137363	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56953348	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67502261	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71423356	0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7143858	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7145944	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7147362	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7147710	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7159476	0.83[ASN][1000 genomes]
rs8012954	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8014890	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8015317	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8015425	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8016781	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs959242	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456334	chr14:69793624-69831037	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv564966	chr14:69793624-69831037	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58553067	SLC39A9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69815600-69838800	Weak transcription	Brain Germinal Matrix	brain
2	chr14:69817600-69823000	Enhancers	Primary B cells from peripheral blood	blood
3	chr14:69818400-69827400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr14:69818600-69842800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr14:69820400-69823000	Enhancers	Primary B cells from cord blood	blood
6	chr14:69820600-69823000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr14:69820800-69823200	Enhancers	Fetal Muscle Leg	muscle
8	chr14:69820800-69823200	Weak transcription	Gastric	stomach
9	chr14:69821000-69823200	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr14:69821000-69838800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr14:69821000-69839600	Weak transcription	Fetal Brain Female	brain
12	chr14:69821200-69823000	Enhancers	Fetal Muscle Trunk	muscle
13	chr14:69821200-69823000	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr14:69821200-69823200	Enhancers	NHDF-Ad	bronchial
15	chr14:69821200-69825400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr14:69821400-69823000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr14:69821400-69823200	Enhancers	Rectal Smooth Muscle	rectum
18	chr14:69821400-69824200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr14:69821600-69823000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr14:69821600-69823200	Enhancers	Colon Smooth Muscle	Colon
21	chr14:69821600-69823600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr14:69821800-69823000	Enhancers	Brain Hippocampus Middle	brain
23	chr14:69821800-69823200	Enhancers	Stomach Smooth Muscle	stomach
24	chr14:69821800-69824200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr14:69821800-69827200	Weak transcription	Fetal Intestine Small	intestine
26	chr14:69821800-69852400	Weak transcription	Spleen	Spleen
27	chr14:69822000-69823200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr14:69822000-69829600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr14:69822200-69823000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr14:69822200-69823000	Enhancers	Right Ventricle	heart
31	chr14:69822200-69823200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr14:69822200-69823200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr14:69822200-69823200	Enhancers	Muscle Satellite Cultured Cells	--
34	chr14:69822200-69823200	Enhancers	HSMMtube	muscle
35	chr14:69822200-69823200	Enhancers	Osteobl	bone
36	chr14:69822200-69823800	Weak transcription	Esophagus	oesophagus
37	chr14:69822200-69824000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr14:69822400-69823000	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr14:69822400-69823000	Enhancers	Adipose Nuclei	Adipose
40	chr14:69822400-69823000	Enhancers	HSMM	muscle
41	chr14:69822400-69823000	Enhancers	NH-A	brain
42	chr14:69822400-69823200	Enhancers	Left Ventricle	heart
43	chr14:69822400-69823200	Enhancers	GM12878-XiMat	blood
44	chr14:69822400-69823800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr14:69822400-69824000	Enhancers	NHLF	lung
46	chr14:69822600-69823000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr14:69822600-69823000	Enhancers	Fetal Stomach	stomach
48	chr14:69822600-69823200	Enhancers	Brain Angular Gyrus	brain
49	chr14:69822600-69825800	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr14:69822800-69823000	Enhancers	Brain Anterior Caudate	brain

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