Variant report

Variant	rs55963294
Chromosome Location	chr1:153543682-153543683
allele	C/T
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:21)
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	HNF4G	chr1:153543465-153543725	HepG2	liver:	n/a	chr1:153543589-153543604

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153505702..153508761-chr1:153542636..153545850,4	MCF-7	breast:
2	chr1:153517548..153519270-chr1:153543397..153544994,2	MCF-7	breast:
3	chr1:153541191..153544684-chr1:153594586..153597033,3	MCF-7	breast:
4	chr1:153535304..153546939-chr1:153598248..153612195,40	MCF-7	breast:
5	chr1:153542754..153545208-chr1:153615571..153617361,2	MCF-7	breast:
6	chr1:153543345..153545167-chr1:153640318..153643293,2	MCF-7	breast:
7	chr1:153533881..153554060-chr1:153575339..153590405,58	MCF-7	breast:
8	chr1:153537061..153539432-chr1:153543087..153544753,2	K562	blood:
9	chr1:153543546..153546056-chr1:153550491..153552553,3	MCF-7	breast:
10	chr1:153334961..153337915-chr1:153541192..153545009,3	MCF-7	breast:
11	chr1:153539127..153551919-chr1:153598146..153608314,34	MCF-7	breast:
12	chr1:153542770..153546215-chr1:153620036..153623245,5	MCF-7	breast:
13	chr1:153538796..153540842-chr1:153542401..153545642,3	MCF-7	breast:
14	chr1:153542610..153547535-chr1:153612482..153617138,6	MCF-7	breast:
15	chr1:153540517..153543717-chr1:153544324..153546793,4	K562	blood:
16	chr1:153543436..153546067-chr1:153630081..153632801,2	MCF-7	breast:
17	chr1:153543619..153547202-chr1:153580802..153586439,10	MCF-7	breast:
18	chr1:153543568..153545263-chr1:153747751..153750301,2	MCF-7	breast:
19	chr1:153502286..153504111-chr1:153542207..153544551,2	MCF-7	breast:
20	chr1:153543081..153545945-chr1:153646440..153648834,2	MCF-7	breast:
21	chr1:153542217..153544092-chr1:153545232..153547357,2	K562	blood:

No data

Variant related genes	Relation type
S100A2	TF binding region
ENSG00000196754	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000160678	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000189334	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000143553	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000143554	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs16835464	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28636749	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28715047	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55815414	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57034503	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs60069797	0.85[EUR][1000 genomes]
rs9660988	0.84[EUR][1000 genomes]
rs9662163	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9662917	0.96[EUR][1000 genomes]
rs9728377	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9729105	1.00[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	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS 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 miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153539000-153545600	Weak transcription	Small Intestine	intestine
2	chr1:153539600-153554000	Weak transcription	Ovary	ovary
3	chr1:153540800-153545800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:153541000-153544400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:153541000-153546600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:153541200-153545600	Weak transcription	Gastric	stomach
7	chr1:153541400-153544400	Weak transcription	Primary B cells from cord blood	blood
8	chr1:153541400-153544600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr1:153541400-153544600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:153541400-153545000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:153541400-153545000	Weak transcription	GM12878-XiMat	blood
12	chr1:153541400-153545200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:153541400-153545200	Weak transcription	Brain Angular Gyrus	brain
14	chr1:153541400-153547400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:153541600-153544000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:153541600-153544000	Weak transcription	Osteobl	bone
17	chr1:153541600-153544200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:153541600-153544200	Weak transcription	Brain Anterior Caudate	brain
19	chr1:153541600-153544200	Weak transcription	Esophagus	oesophagus
20	chr1:153541600-153544200	Weak transcription	HSMM	muscle
21	chr1:153541600-153544200	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr1:153541600-153544200	Weak transcription	NH-A	brain
23	chr1:153541600-153544200	Weak transcription	NHLF	lung
24	chr1:153541600-153544400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:153541600-153544400	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr1:153541600-153544400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:153541600-153544400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:153541600-153544600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:153541600-153544800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:153541600-153544800	Weak transcription	Primary B cells from peripheral blood	blood
31	chr1:153541600-153544800	Weak transcription	Fetal Heart	heart
32	chr1:153541600-153544800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr1:153541600-153544800	Weak transcription	Stomach Mucosa	stomach
34	chr1:153541600-153545000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:153541600-153545000	Weak transcription	Adipose Nuclei	Adipose
36	chr1:153541600-153545000	Weak transcription	Spleen	Spleen
37	chr1:153541600-153545000	Weak transcription	HUVEC	blood vessel
38	chr1:153541600-153545200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:153541600-153545200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:153541600-153545200	Weak transcription	Brain Substantia Nigra	brain
41	chr1:153541600-153545200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr1:153541600-153545200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr1:153541600-153545400	Weak transcription	Colon Smooth Muscle	Colon
44	chr1:153541600-153545600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:153541600-153550200	Weak transcription	Right Atrium	heart
46	chr1:153541800-153544200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:153541800-153544200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:153541800-153544200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr1:153541800-153544200	Weak transcription	K562	blood
50	chr1:153541800-153544200	Weak transcription	NHDF-Ad	bronchial

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