Variant report

Variant	rs56341880
Chromosome Location	chr1:150978741-150978742
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:43)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:43 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:150978508-150979653	PBDE	blood:	n/a	n/a
2	MXI1	chr1:150978548-150979637	HepG2	liver:	n/a	n/a
3	CTCF	chr1:150978220-150979806	SK-N-SH	brain:	n/a	chr1:150978700-150978708
4	HEY1	chr1:150978723-150979773	HepG2	liver:	n/a	n/a
5	ELF1	chr1:150978641-150979216	GM12878	blood:	n/a	n/a
6	TBP	chr1:150978488-150979635	Hela-S3	cervix:	n/a	n/a
7	GTF2F1	chr1:150978434-150979594	Hela-S3	cervix:	n/a	n/a
8	RCOR1	chr1:150978057-150979578	K562	blood:	n/a	n/a
9	GATA2	chr1:150978393-150979298	SH-SY5Y	brain:	n/a	n/a
10	CTCF	chr1:150978600-150978750	GM06990	blood:	n/a	chr1:150978700-150978708
11	ELF1	chr1:150978379-150979779	MCF-7	breast:	n/a	n/a
12	SIN3AK20	chr1:150978184-150981996	MCF-7	breast:	n/a	n/a
13	POLR2A	chr1:150978731-150979599	HUVEC	blood vessel:	n/a	n/a
14	KAP1	chr1:150978188-150979637	HEK293	kidney:	n/a	n/a
15	CTCF	chr1:150978718-150979680	MCF-7	breast:	n/a	n/a
16	POLR2A	chr1:150978695-150981793	HepG2	liver:	n/a	n/a
17	MAX	chr1:150978104-150979664	MCF-7	breast:	n/a	chr1:150978137-150978147
18	ZNF263	chr1:150978072-150979583	HEK293-T-REx	kidney:	n/a	chr1:150978355-150978364
19	RUNX3	chr1:150978704-150979545	GM12878	blood:	n/a	n/a
20	MXI1	chr1:150978177-150979784	SK-N-SH	brain:	n/a	n/a
21	SIN3A	chr1:150978652-150979523	H1-hESC	embryonic stem cell:	n/a	n/a
22	ELF1	chr1:150978473-150979686	MCF-7	breast:	n/a	n/a
23	CTCF	chr1:150978191-150979776	A549	lung:	n/a	chr1:150978700-150978708
24	MTA3	chr1:150978602-150979513	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:150978694-150979491	Hela-S3	cervix:	n/a	n/a
26	RAD21	chr1:150978544-150979677	SK-N-SH	brain:	n/a	n/a
27	RCOR1	chr1:150978741-150979500	Hela-S3	cervix:	n/a	n/a
28	MAX	chr1:150978610-150979554	Hela-S3	cervix:	n/a	n/a
29	MAZ	chr1:150978492-150979569	K562	blood:	n/a	n/a
30	FOXA1	chr1:150978714-150979698	HepG2	liver:	n/a	n/a
31	CTCF	chr1:150978700-150978850	HCM	heart:	n/a	chr1:150978700-150978708
32	CTCF	chr1:150978720-150978870	MCF-7	breast:	n/a	n/a
33	RFX5	chr1:150978702-150979556	Hela-S3	cervix:	n/a	n/a
34	REST	chr1:150978469-150979746	H1-neurons	neurons:	n/a	chr1:150978544-150978553 chr1:150978691-150978704
35	CTCF	chr1:150978720-150978870	GM12864	blood:	n/a	n/a
36	GATA3	chr1:150978434-150979049	T-47D	breast:	n/a	n/a
37	WRNIP1	chr1:150978630-150978809	GM12878	blood:	n/a	n/a
38	ESR1	chr1:150978332-150978751	T-47D	breast:	n/a	n/a
39	ELF1	chr1:150978732-150979528	HepG2	liver:	n/a	n/a
40	CTCF	chr1:150978720-150978870	GM12873	blood:	n/a	n/a
41	GATA3	chr1:150978565-150979015	SH-SY5Y	brain:	n/a	n/a
42	MAZ	chr1:150978535-150979523	Hela-S3	cervix:	n/a	n/a
43	MXI1	chr1:150978725-150979565	Hela-S3	cervix:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150975371..150978821-chr1:151041337..151043536,3	K562	blood:
2	chr1:150974834..150982774-chr1:151014282..151023779,19	MCF-7	breast:
3	chr1:150550535..150554049-chr1:150976755..150981799,6	K562	blood:
4	chr1:150532436..150535638-chr1:150978193..150982152,3	MCF-7	breast:
5	chr1:150976422..150979249-chr1:151029519..151032163,2	MCF-7	breast:
6	chr1:150963797..150966620-chr1:150976784..150978920,2	K562	blood:
7	chr1:150976003..150979092-chr1:151029150..151032179,4	K562	blood:
8	chr1:150978249..150978749-chr10:104404134..104404864,2	NB4	blood:
9	chr1:150954595..150956267-chr1:150977879..150980277,2	K562	blood:
10	chr1:150944222..150949507-chr1:150975860..150982521,8	K562	blood:
11	chr1:150977224..150980859-chr1:151016149..151020552,4	K562	blood:
12	chr1:150950114..150953759-chr1:150976393..150978885,3	K562	blood:
13	chr1:150977352..150978939-chr1:151168361..151170660,2	K562	blood:
14	chr1:150942078..150949693-chr1:150976791..150984782,24	MCF-7	breast:
15	chr1:150952182..150958148-chr1:150976816..150982947,12	MCF-7	breast:
16	chr1:150978624..150980808-chr1:151042705..151044650,2	MCF-7	breast:
17	chr1:150976577..150980080-chr1:150980788..150983027,4	MCF-7	breast:
18	chr1:150977392..150983338-chr1:151040807..151046211,16	MCF-7	breast:
19	chr1:150976723..150987587-chr1:151024685..151036322,24	MCF-7	breast:
20	chr1:150954001..150954567-chr1:150978085..150978829,2	MCF-7	breast:

No data

Variant related genes	Relation type
PRUNE	TF binding region
ENSG00000143458	Chromatin interaction
ENSG00000163141	Chromatin interaction
ENSG00000143418	Chromatin interaction
ENSG00000171206	Chromatin interaction
ENSG00000213190	Chromatin interaction
ENSG00000143443	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000231073	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000143412	Chromatin interaction
ENSG00000203804	Chromatin interaction
ENSG00000143384	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10157132	0.89[AMR][1000 genomes]
rs12090632	0.89[AMR][1000 genomes]
rs12097548	0.89[AMR][1000 genomes]
rs16832391	0.89[AMR][1000 genomes]
rs55884154	0.89[AMR][1000 genomes]
rs57376891	0.89[AMR][1000 genomes]
rs57378704	0.89[AMR][1000 genomes]
rs57746902	0.89[AMR][1000 genomes]
rs58338969	0.89[AMR][1000 genomes]
rs59703669	0.89[AMR][1000 genomes]
rs6672625	0.89[AMR][1000 genomes]
rs6674452	0.89[AMR][1000 genomes]
rs6703303	0.89[AMR][1000 genomes]
rs74127060	0.89[AMR][1000 genomes]
rs74127063	0.89[AMR][1000 genomes]
rs74127089	0.89[AMR][1000 genomes]
rs74127091	0.89[AMR][1000 genomes]
rs74127092	0.89[AMR][1000 genomes]
rs74128604	0.89[AMR][1000 genomes]
rs74128609	0.89[AMR][1000 genomes]
rs7522741	0.89[AMR][1000 genomes]
rs7547614	0.89[AMR][1000 genomes]
rs9988459	0.89[AMR][1000 genomes]
rs9988521	0.89[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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150955400-150978800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:150973600-150980800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr1:150973800-150979000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr1:150974800-150979000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
5	chr1:150975400-150982400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:150975800-150979600	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr1:150976400-150979600	Active TSS	Pancreas	Pancrea
8	chr1:150976600-150978800	Active TSS	Primary T killer memory cells from peripheral blood	blood
9	chr1:150976800-150979600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr1:150977000-150979200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:150977000-150979400	Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr1:150977000-150979400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:150977000-150979400	Active TSS	Brain Anterior Caudate	brain
14	chr1:150977000-150979400	Active TSS	Brain Hippocampus Middle	brain
15	chr1:150977000-150979400	Active TSS	Brain Substantia Nigra	brain
16	chr1:150977000-150979400	Active TSS	Colonic Mucosa	Colon
17	chr1:150977000-150979400	Active TSS	Rectal Smooth Muscle	rectum
18	chr1:150977000-150980000	Active TSS	HepG2	liver
19	chr1:150977200-150979400	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr1:150977200-150979400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:150977200-150979400	Active TSS	Ovary	ovary
22	chr1:150977200-150979600	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr1:150977200-150979600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:150977200-150979600	Active TSS	Right Atrium	heart
25	chr1:150977200-150979800	Flanking Active TSS	HMEC	breast
26	chr1:150977400-150979000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr1:150977400-150979000	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr1:150977400-150979000	Flanking Active TSS	Liver	Liver
29	chr1:150977400-150979000	Flanking Active TSS	Hela-S3	cervix
30	chr1:150977400-150979400	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr1:150977400-150979400	Active TSS	Fetal Kidney	kidney
32	chr1:150977400-150979600	Active TSS	Left Ventricle	heart
33	chr1:150977400-150979800	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr1:150977400-150979800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr1:150977400-150980600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr1:150977400-150981800	Active TSS	Esophagus	oesophagus
37	chr1:150977600-150978800	Enhancers	Placenta Amnion	Placenta Amnion
38	chr1:150977600-150979000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:150977600-150979400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:150977600-150979400	Active TSS	Brain Cingulate Gyrus	brain
41	chr1:150977600-150979400	Active TSS	Colon Smooth Muscle	Colon
42	chr1:150977600-150979400	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr1:150977600-150979400	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr1:150977600-150979400	Active TSS	Stomach Smooth Muscle	stomach
45	chr1:150977600-150979600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr1:150977600-150979600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr1:150977600-150979600	Active TSS	Fetal Intestine Large	intestine
48	chr1:150977600-150979600	Flanking Active TSS	Fetal Muscle Leg	muscle
49	chr1:150977600-150979600	Active TSS	Right Ventricle	heart
50	chr1:150977600-150980000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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