Variant report

Variant	rs6450023
Chromosome Location	chr5:68526063-68526064
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr5:68526039-68526415	MCF10A-Er-Src	breast:	n/a	chr5:68526225-68526237 chr5:68526226-68526236 chr5:68526226-68526236 chr5:68526226-68526235 chr5:68526226-68526236 chr5:68526226-68526236
2	FOXA1	chr5:68525909-68526269	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:68523954..68526904-chr5:68529417..68531065,2	MCF-7	breast:
2	chr5:68524400..68526328-chr5:68527569..68529446,2	K562	blood:

Variant related genes	Relation type
CDK7	TF binding region
ENSG00000134058	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2069433	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs338685	0.80[JPT][hapmap]
rs7380054	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7707153	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7707347	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][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	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv3378789	chr5:68438275-68540725	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6450023	TNPO1	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68514200-68530200	Weak transcription	Small Intestine	intestine
2	chr5:68514200-68530200	Weak transcription	Spleen	Spleen
3	chr5:68514400-68530200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:68514400-68530200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:68514400-68530200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:68514400-68530200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:68514400-68530200	Weak transcription	Aorta	Aorta
8	chr5:68514400-68530200	Weak transcription	Esophagus	oesophagus
9	chr5:68514400-68530200	Weak transcription	Gastric	stomach
10	chr5:68514400-68530200	Weak transcription	Pancreas	Pancrea
11	chr5:68514400-68530200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr5:68514800-68530000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr5:68515000-68530000	Weak transcription	Psoas Muscle	Psoas
14	chr5:68515200-68529800	Weak transcription	Fetal Brain Female	brain
15	chr5:68515200-68529800	Weak transcription	NHLF	lung
16	chr5:68515200-68530000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr5:68515200-68530000	Weak transcription	Fetal Brain Male	brain
18	chr5:68515200-68530000	Weak transcription	Fetal Kidney	kidney
19	chr5:68515200-68530000	Weak transcription	Fetal Lung	lung
20	chr5:68515400-68529400	Weak transcription	Fetal Heart	heart
21	chr5:68515400-68529800	Weak transcription	Brain Anterior Caudate	brain
22	chr5:68515400-68529800	Weak transcription	Colon Smooth Muscle	Colon
23	chr5:68515400-68529800	Weak transcription	Hela-S3	cervix
24	chr5:68515400-68530000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:68515400-68530000	Weak transcription	Right Ventricle	heart
26	chr5:68515600-68530000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:68515600-68530000	Weak transcription	Brain Substantia Nigra	brain
28	chr5:68515800-68530000	Weak transcription	Brain Angular Gyrus	brain
29	chr5:68520200-68526400	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr5:68520400-68526400	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr5:68520400-68526600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:68520400-68528200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr5:68520800-68529800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr5:68520800-68530200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:68521000-68526400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr5:68521000-68526400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:68521400-68526400	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr5:68521800-68526400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:68521800-68526800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:68521800-68530200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr5:68522000-68526200	Strong transcription	Fetal Intestine Large	intestine
42	chr5:68522200-68526400	Strong transcription	Fetal Thymus	thymus
43	chr5:68522800-68526200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr5:68522800-68526400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:68522800-68526400	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr5:68522800-68526400	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr5:68522800-68526400	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr5:68522800-68526400	Strong transcription	Dnd41	blood
49	chr5:68522800-68527400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr5:68523000-68526200	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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