Variant report

Variant	rs10888420
Chromosome Location	chr1:151488153-151488154
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:151488144-151489071	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151428938..151433041-chr1:151480813..151490135,53	MCF-7	breast:
2	chr1:151449677..151451707-chr1:151487320..151488913,2	MCF-7	breast:
3	chr1:151481429..151491154-chr1:151502501..151517487,49	MCF-7	breast:
4	chr1:151487501..151489912-chr1:151498900..151500464,2	K562	blood:
5	chr1:151481542..151488437-chr1:151515636..151525415,14	MCF-7	breast:
6	chr1:151388224..151390291-chr1:151485508..151488200,2	MCF-7	breast:
7	chr1:151484895..151488476-chr1:151501295..151502821,3	MCF-7	breast:
8	chr1:151477348..151494376-chr1:151504804..151515249,50	MCF-7	breast:
9	chr1:151487415..151491169-chr1:151814184..151816994,3	MCF-7	breast:
10	chr1:151427202..151436068-chr1:151477865..151490153,60	MCF-7	breast:

No data

Variant related genes	Relation type
CGN	TF binding region
ENSG00000143375	Chromatin interaction
ENSG00000207606	Chromatin interaction
ENSG00000252840	Chromatin interaction
ENSG00000143442	Chromatin interaction
ENSG00000234614	Chromatin interaction
ENSG00000201134	Chromatin interaction
ENSG00000232536	Chromatin interaction
ENSG00000143367	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10749663	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2337361	0.87[AMR][1000 genomes]
rs6587599	1.00[AMR][1000 genomes]
rs7516311	0.87[AMR][1000 genomes]
rs7533032	1.00[AMR][1000 genomes]
rs7540498	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151484600-151512000	Weak transcription	Right Atrium	heart
2	chr1:151484800-151491200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:151485000-151492400	Weak transcription	Ovary	ovary
4	chr1:151485200-151511800	Weak transcription	Fetal Brain Female	brain
5	chr1:151485400-151491000	Weak transcription	Gastric	stomach
6	chr1:151485600-151489000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:151485600-151491200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:151485800-151488800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:151485800-151488800	Enhancers	Placenta Amnion	Placenta Amnion
10	chr1:151485800-151490000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:151485800-151491400	Weak transcription	Brain Angular Gyrus	brain
12	chr1:151485800-151491400	Weak transcription	Brain Substantia Nigra	brain
13	chr1:151485800-151511800	Weak transcription	Brain Germinal Matrix	brain
14	chr1:151485800-151512200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:151486000-151491200	Weak transcription	Brain Anterior Caudate	brain
16	chr1:151486000-151501800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:151486200-151491200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:151486400-151489200	Enhancers	H1 Cell Line	embryonic stem cell
19	chr1:151486400-151491200	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:151486600-151488600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:151486600-151491000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:151486600-151492000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:151486600-151511800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:151486800-151489000	Enhancers	Pancreas	Pancrea
25	chr1:151486800-151491200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:151486800-151512200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:151487000-151488400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:151487000-151488400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:151487000-151488600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:151487000-151488800	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr1:151487000-151488800	Enhancers	Colonic Mucosa	Colon
32	chr1:151487000-151491000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:151487000-151501800	Weak transcription	Esophagus	oesophagus
34	chr1:151487000-151511800	Weak transcription	Small Intestine	intestine
35	chr1:151487200-151488200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:151487200-151488400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:151487200-151488400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:151487200-151488400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:151487200-151488400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:151487200-151488400	Weak transcription	A549	lung
41	chr1:151487200-151489000	Enhancers	HepG2	liver
42	chr1:151487200-151502400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr1:151487400-151488200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr1:151487400-151488400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:151487400-151488400	Weak transcription	Placenta	Placenta
46	chr1:151487400-151488400	Weak transcription	HMEC	breast
47	chr1:151487400-151488600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr1:151487400-151490000	Enhancers	Liver	Liver
49	chr1:151487400-151490400	Enhancers	Fetal Intestine Large	intestine
50	chr1:151487400-151492000	Weak transcription	Fetal Kidney	kidney

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