Variant report

Variant	rs2280643
Chromosome Location	chr2:74358286-74358287
allele	C/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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:74345800..74349275-chr2:74357385..74359321,6	MCF-7	breast:
2	chr2:74357697..74362841-chr2:74424131..74428670,5	K562	blood:
3	chr2:74356615..74359477-chr2:74372011..74374139,2	MCF-7	breast:
4	chr2:74285218..74287266-chr2:74357972..74359990,2	K562	blood:
5	chr2:74224937..74227638-chr2:74357477..74359947,2	MCF-7	breast:
6	chr2:74235618..74237940-chr2:74357623..74360543,2	MCF-7	breast:
7	chr2:74356708..74358883-chr2:74362646..74364530,2	MCF-7	breast:
8	chr2:74210918..74212665-chr2:74357393..74359886,2	MCF-7	breast:
9	chr2:74347023..74350379-chr2:74357531..74361133,4	K562	blood:
10	chr2:74357599..74359894-chr2:74425001..74426947,2	K562	blood:
11	chr2:74356810..74359552-chr2:74365465..74371208,7	MCF-7	breast:
12	chr2:73906056..73907836-chr2:74356105..74358909,2	MCF-7	breast:
13	chr2:74356746..74359023-chr2:74373471..74375958,3	MCF-7	breast:
14	chr2:74356833..74358687-chr2:74404126..74407043,2	K562	blood:
15	chr2:74357326..74359137-chr2:74360563..74363969,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257800	Chromatin interaction
ENSG00000065911	Chromatin interaction
ENSG00000225439	Chromatin interaction
ENSG00000114978	Chromatin interaction
ENSG00000235499	Chromatin interaction
ENSG00000217702	Chromatin interaction
ENSG00000163170	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11675066	0.95[ASN][1000 genomes]
rs12478482	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12619982	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2122290	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2177707	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2280642	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280644	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4429500	0.86[EUR][1000 genomes]
rs4452177	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4563249	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4852329	0.93[ASN][1000 genomes]
rs4853010	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4853011	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4853012	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58759652	0.85[EUR][1000 genomes]
rs59570457	0.86[EUR][1000 genomes]
rs60330274	0.86[EUR][1000 genomes]
rs60705299	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60964317	0.85[EUR][1000 genomes]
rs61521879	0.84[EUR][1000 genomes]
rs6707619	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6715351	0.86[EUR][1000 genomes]
rs6731793	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72911122	0.86[EUR][1000 genomes]
rs72915068	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7576762	0.84[AFR][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	nsv874286	chr2:74323500-74436721	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv3427010	chr2:74351730-74813541	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2280643	MGC10955	cis	Skin Sun Exposed Lower leg	GTEx
rs2280643	FNBP1P1	cis	Skin Sun Exposed Lower leg	GTEx
rs2280643	MGC10955	cis	Adipose Subcutaneous	GTEx
rs2280643	FNBP1P1	cis	Artery Aorta	GTEx
rs2280643	MGC10955	cis	Esophagus Mucosa	GTEx
rs2280643	FNBP1P1	cis	Artery Tibial	GTEx
rs2280643	MGC10955	cis	Artery Tibial	GTEx
rs2280643	MGC10955	cis	Artery Aorta	GTEx
rs2280643	FNBP1P1	cis	Stomach	GTEx
rs2280643	MGC10955	cis	Thyroid	GTEx
rs2280643	MGC10955	cis	Nerve Tibial	GTEx
rs2280643	MGC10955	cis	lung	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74348200-74360400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:74348200-74367600	Weak transcription	Brain Anterior Caudate	brain
3	chr2:74348600-74361800	Weak transcription	Hela-S3	cervix
4	chr2:74348800-74360400	Weak transcription	Primary T cells from cord blood	blood
5	chr2:74350800-74360400	Weak transcription	Brain Substantia Nigra	brain
6	chr2:74351200-74358400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:74353400-74360400	Weak transcription	Dnd41	blood
8	chr2:74353600-74360400	Weak transcription	A549	lung
9	chr2:74354200-74359400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:74354400-74373800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:74354800-74360400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:74355200-74373800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:74356400-74361400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:74357000-74360400	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:74357200-74361200	Weak transcription	NHLF	lung
16	chr2:74357600-74359400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:74357600-74361200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:74357600-74361200	Weak transcription	Fetal Thymus	thymus
19	chr2:74357600-74361800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:74357600-74361800	Weak transcription	Right Ventricle	heart
21	chr2:74357600-74373800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr2:74357800-74360400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:74357800-74360400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:74357800-74361200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:74357800-74361400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:74357800-74361800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr2:74357800-74367600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr2:74357800-74373600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:74358000-74360400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:74358000-74361200	Weak transcription	HMEC	breast
31	chr2:74358000-74361600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:74358200-74358600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr2:74358200-74358600	Enhancers	K562	blood
34	chr2:74358200-74360400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:74358200-74360600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr2:74358200-74361600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr2:74358200-74364800	Weak transcription	Esophagus	oesophagus
38	chr2:74358200-74373800	Weak transcription	Placenta Amnion	Placenta Amnion

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