Variant report

Variant	rs55935377
Chromosome Location	chr1:151019778-151019779
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:151019747-151029675	K562	blood:	n/a	n/a
2	MAX	chr1:151019763-151021510	MCF-7	breast:	n/a	n/a
3	MXI1	chr1:151019631-151021552	IMR90	lung:	n/a	n/a
4	POLR2A	chr1:151019738-151021738	HUVEC	blood vessel:	n/a	n/a
5	MXI1	chr1:151019703-151021637	SK-N-SH	brain:	n/a	n/a
6	SIN3AK20	chr1:151019710-151021753	MCF-7	breast:	n/a	n/a
7	MAX	chr1:151019693-151021514	A549	lung:	n/a	n/a
8	POLR2A	chr1:151019736-151024166	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr1:151019768-151021610	H1-hESC	embryonic stem cell:	n/a	n/a
10	TCF12	chr1:151019722-151021429	A549	lung:	n/a	n/a
11	POLR2A	chr1:151019772-151021526	HepG2	liver:	n/a	n/a
12	PML	chr1:151019769-151021450	MCF-7	breast:	n/a	n/a
13	POLR2A	chr1:151019761-151021627	PFSK-1	brain:	n/a	n/a
14	CTCF	chr1:151019645-151021504	A549	lung:	n/a	n/a
15	HDAC2	chr1:151019674-151021450	MCF-7	breast:	n/a	chr1:151020174-151020183
16	MAZ	chr1:151019778-151021398	IMR90	lung:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150979769..150983967-chr1:151018069..151024059,8	MCF-7	breast:
2	chr1:151019258..151021349-chr6:16128728..16130592,2	MCF-7	breast:
3	chr1:151008538..151012828-chr1:151019200..151022428,4	K562	blood:
4	chr1:150995615..151002939-chr1:151018225..151024612,15	MCF-7	breast:
5	chr1:150974834..150982774-chr1:151014282..151023779,19	MCF-7	breast:
6	chr1:150977224..150980859-chr1:151016149..151020552,4	K562	blood:
7	chr1:151019236..151020800-chr1:151137402..151139572,2	K562	blood:
8	chr1:150943913..150947004-chr1:151018258..151022109,4	MCF-7	breast:

No data

Variant related genes	Relation type
C1orf56	TF binding region
ENSG00000143409	Chromatin interaction
ENSG00000143418	Chromatin interaction
ENSG00000163141	Chromatin interaction
ENSG00000231073	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000163155	Chromatin interaction
ENSG00000007944	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs41299635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41310891	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55716130	1.00[AMR][1000 genomes]
rs57330524	1.00[AMR][1000 genomes]
rs58618837	1.00[AMR][1000 genomes]
rs58763463	1.00[AMR][1000 genomes]
rs59737164	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60636837	1.00[AMR][1000 genomes]
rs60865304	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74125051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74125053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74125059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74125062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74125063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74125065	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74125077	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74125079	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74125080	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74125087	1.00[AMR][1000 genomes]
rs74125088	1.00[AMR][1000 genomes]
rs74125093	1.00[AMR][1000 genomes]
rs74127505	1.00[AMR][1000 genomes]
rs74127506	1.00[AMR][1000 genomes]
rs74127513	1.00[AMR][1000 genomes]
rs74127514	1.00[AMR][1000 genomes]
rs74127515	1.00[AMR][1000 genomes]
rs74127528	1.00[AMR][1000 genomes]
rs74127529	1.00[AMR][1000 genomes]
rs74127530	1.00[AMR][1000 genomes]
rs74127531	1.00[AMR][1000 genomes]
rs74127535	1.00[AMR][1000 genomes]
rs74127536	1.00[AMR][1000 genomes]
rs74127539	1.00[AMR][1000 genomes]
rs74127540	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	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:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150997600-151019800	Weak transcription	HUVEC	blood vessel
2	chr1:150997800-151019800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:151000000-151019800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:151000000-151019800	Weak transcription	NHLF	lung
5	chr1:151000200-151019800	Weak transcription	Small Intestine	intestine
6	chr1:151003800-151019800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr1:151004400-151019800	Weak transcription	Fetal Kidney	kidney
8	chr1:151006800-151019800	Weak transcription	Gastric	stomach
9	chr1:151006800-151019800	Weak transcription	HepG2	liver
10	chr1:151007200-151019800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:151007200-151019800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:151007400-151019800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:151007400-151019800	Weak transcription	Brain Angular Gyrus	brain
14	chr1:151007400-151019800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:151008000-151019800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:151008000-151019800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:151008000-151019800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:151008000-151019800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:151008000-151019800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr1:151008000-151019800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:151008000-151019800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:151008000-151019800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:151008000-151019800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:151008000-151019800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:151008000-151019800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:151008000-151019800	Weak transcription	Brain Germinal Matrix	brain
27	chr1:151008000-151019800	Weak transcription	Brain Hippocampus Middle	brain
28	chr1:151008000-151019800	Weak transcription	Fetal Lung	lung
29	chr1:151008000-151019800	Weak transcription	Ovary	ovary
30	chr1:151008000-151019800	Weak transcription	Pancreas	Pancrea
31	chr1:151008000-151019800	Weak transcription	Psoas Muscle	Psoas
32	chr1:151008000-151019800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr1:151008000-151019800	Weak transcription	Thymus	Thymus
34	chr1:151008000-151020000	Weak transcription	Aorta	Aorta
35	chr1:151008000-151020000	Weak transcription	Left Ventricle	heart
36	chr1:151008000-151020000	Weak transcription	Right Ventricle	heart
37	chr1:151008000-151020200	Weak transcription	Lung	lung
38	chr1:151008200-151019800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:151008200-151019800	Weak transcription	Adipose Nuclei	Adipose
40	chr1:151008200-151019800	Weak transcription	Brain Anterior Caudate	brain
41	chr1:151008200-151019800	Weak transcription	HSMM	muscle
42	chr1:151009400-151019800	Weak transcription	Liver	Liver
43	chr1:151009400-151019800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:151009400-151019800	Weak transcription	HMEC	breast
45	chr1:151009600-151019800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr1:151010000-151019800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:151011600-151020000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:151011800-151019800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:151012200-151019800	Weak transcription	Placenta	Placenta
50	chr1:151012400-151019800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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