Variant report

Variant	rs41285577
Chromosome Location	chr5:177580643-177580644
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr5:177580540-177581049	GM12878	blood:	n/a	chr5:177580924-177580933
2	YY1	chr5:177580582-177581143	HepG2	liver:	n/a	n/a
3	BCL3	chr5:177579967-177581173	A549	lung:	n/a	chr5:177581091-177581100 chr5:177581068-177581077
4	SP1	chr5:177580583-177581186	H1-hESC	embryonic stem cell:	n/a	chr5:177581091-177581100 chr5:177580997-177581008 chr5:177581089-177581101 chr5:177581119-177581131 chr5:177581121-177581130 chr5:177580994-177581008 chr5:177580997-177581009 chr5:177580923-177580944 chr5:177581120-177581130 chr5:177581120-177581129 chr5:177581086-177581100 chr5:177581116-177581130 chr5:177581119-177581131 chr5:177581089-177581101 chr5:177580997-177581009
5	POLR2A	chr5:177580553-177581010	A549	lung:	n/a	n/a
6	ZNF263	chr5:177579320-177581131	HEK293-T-REx	kidney:	n/a	n/a
7	GATA3	chr5:177579439-177581182	MCF-7	breast:	n/a	n/a
8	CREB1	chr5:177580604-177581283	K562	blood:	n/a	n/a
9	POLR2A	chr5:177580531-177581229	GM15510	blood:	n/a	n/a
10	SRF	chr5:177580279-177581283	HCT-116	colon:	n/a	chr5:177581120-177581130
11	PML	chr5:177576624-177580747	MCF-7	breast:	n/a	n/a
12	GABPA	chr5:177580366-177581277	MCF-7	breast:	n/a	n/a
13	ETS1	chr5:177580485-177580991	K562	blood:	n/a	n/a
14	GABPA	chr5:177580632-177581238	A549	lung:	n/a	n/a
15	POLR2A	chr5:177580545-177581261	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr5:177580575-177581184	K562	blood:	n/a	n/a
17	POLR2A	chr5:177580498-177581159	K562	blood:	n/a	n/a
18	MYC	chr5:177580390-177581192	K562	blood:	n/a	chr5:177581120-177581130
19	POLR2A	chr5:177580451-177581124	GM12878	blood:	n/a	n/a
20	POLR2A	chr5:177580569-177581017	GM12891	blood:	n/a	n/a
21	MYC	chr5:177580618-177581155	K562	blood:	n/a	chr5:177581120-177581130
22	MAX	chr5:177580620-177581223	NB4	blood:	n/a	chr5:177581120-177581130
23	NFIC	chr5:177580627-177581134	GM12878	blood:	n/a	n/a
24	POU2F2	chr5:177580577-177581166	GM12891	blood:	n/a	n/a
25	SIN3AK20	chr5:177580531-177581171	SK-N-SH	brain:	n/a	n/a
26	CREB1	chr5:177580445-177581275	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAX	chr5:177580242-177581299	A549	lung:	n/a	chr5:177581120-177581130
28	SIN3AK20	chr5:177580425-177581262	PANC-1	pancreas:	n/a	n/a
29	SIN3AK20	chr5:177576695-177581508	MCF-7	breast:	n/a	n/a
30	POLR2A	chr5:177580331-177581147	U87	brain:	n/a	n/a
31	MXI1	chr5:177580047-177581274	IMR90	lung:	n/a	n/a
32	PML	chr5:177580604-177581147	K562	blood:	n/a	n/a
33	POLR2A	chr5:177576742-177581174	PBDE	blood:	n/a	n/a
34	BRCA1	chr5:177580131-177581151	Hela-S3	cervix:	n/a	n/a
35	ETS1	chr5:177580636-177581158	A549	lung:	n/a	n/a
36	POLR2A	chr5:177580603-177581154	GM18526	blood:	n/a	n/a
37	MYC	chr5:177580634-177581045	MCF-7	breast:	n/a	n/a
38	SPI1	chr5:177580526-177581329	GM12878	blood:	n/a	n/a
39	MYC	chr5:177580402-177581344	A549	lung:	n/a	chr5:177581120-177581130
40	CHD2	chr5:177580008-177581085	H1-hESC	embryonic stem cell:	n/a	n/a
41	MYC	chr5:177580268-177581251	K562	blood:	n/a	chr5:177581120-177581130
42	ELF1	chr5:177580618-177581247	K562	blood:	n/a	n/a
43	POLR2A	chr5:177580610-177581036	K562	blood:	n/a	n/a
44	MAX	chr5:177580337-177581233	ECC-1	luminal epithelium:	n/a	chr5:177581120-177581130
45	YY1	chr5:177580601-177581015	A549	lung:	n/a	n/a
46	GABPA	chr5:177580487-177581254	SK-N-SH	brain:	n/a	n/a
47	TAF1	chr5:177580575-177581031	Hela-S3	cervix:	n/a	n/a
48	REST	chr5:177580383-177581320	H1-neurons	neurons:	n/a	chr5:177581117-177581130
49	POLR2A	chr5:177580452-177581166	GM12892	blood:	n/a	n/a
50	SRF	chr5:177580633-177581213	ECC-1	luminal epithelium:	n/a	chr5:177581120-177581130

No.	Distal block	Cell Line	Cell type
1	chr5:177539791..177542194-chr5:177578689..177582162,4	K562	blood:
2	chr5:177564848..177566469-chr5:177578900..177581118,2	K562	blood:
3	chr5:177539043..177545979-chr5:177577141..177584026,12	K562	blood:
4	chr5:177579578..177582486-chr5:177629664..177632966,4	K562	blood:
5	chr5:177556550..177559096-chr5:177579482..177582645,4	K562	blood:
6	chr20:49575186..49575913-chr5:177580452..177581065,2	MCF-7	breast:
7	chr12:120730631..120732795-chr5:177578874..177580699,2	MCF-7	breast:
8	chr5:177579489..177582257-chr5:177628656..177632410,3	K562	blood:
9	chr5:177578534..177581104-chr5:177631476..177634038,2	MCF-7	breast:
10	chr5:177556214..177559808-chr5:177575521..177582645,10	K562	blood:
11	chr5:177578478..177582579-chr5:177629428..177633237,12	MCF-7	breast:
12	chr5:177578943..177581189-chrX:48438491..48440007,2	MCF-7	breast:

Variant related genes	Relation type
NHP2	TF binding region
ENSG00000228343	Chromatin interaction
ENSG00000124217	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000197451	Chromatin interaction
ENSG00000145911	Chromatin interaction
ENSG00000145916	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs4568380	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4585465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1021198	chr5:177386267-177611648	Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
4	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
5	nsv883190	chr5:177532201-177620189	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv600394	chr5:177549491-177608195	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv1017664	chr5:177578194-177633116	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
8	nsv482872	chr5:177580298-177744381	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	106 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	chr5:177579400-177581400	Active TSS	HSMM	muscle
2	chr5:177579600-177581000	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr5:177579600-177581000	Active TSS	NH-A	brain
4	chr5:177579800-177580800	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr5:177579800-177580800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
6	chr5:177579800-177580800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr5:177579800-177581000	Active TSS	HSMMtube	muscle
8	chr5:177579800-177581400	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr5:177579800-177581400	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr5:177579800-177581400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:177579800-177581400	Active TSS	Fetal Kidney	kidney
12	chr5:177579800-177581800	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr5:177580000-177580800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:177580000-177580800	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr5:177580000-177580800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr5:177580000-177581000	Active TSS	NHDF-Ad	bronchial
17	chr5:177580000-177581200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:177580000-177581200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:177580000-177581400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:177580000-177581400	Active TSS	H9 Cell Line	embryonic stem cell
21	chr5:177580000-177581400	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr5:177580000-177581400	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr5:177580000-177581400	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr5:177580000-177581400	Active TSS	Psoas Muscle	Psoas
25	chr5:177580000-177581400	Active TSS	A549	lung
26	chr5:177580000-177581800	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr5:177580200-177580800	Active TSS	Aorta	Aorta
28	chr5:177580200-177581000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr5:177580200-177581000	Active TSS	Lung	lung
30	chr5:177580200-177581000	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr5:177580200-177581000	Active TSS	Small Intestine	intestine
32	chr5:177580200-177581000	Active TSS	NHEK	skin
33	chr5:177580200-177581000	Active TSS	NHLF	lung
34	chr5:177580200-177581200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr5:177580200-177581200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:177580200-177581200	Active TSS	Stomach Mucosa	stomach
37	chr5:177580200-177581400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:177580200-177581400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr5:177580200-177581400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr5:177580200-177581400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr5:177580200-177581400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:177580200-177581400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr5:177580200-177581400	Active TSS	Muscle Satellite Cultured Cells	--
44	chr5:177580200-177581400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr5:177580200-177581400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr5:177580200-177581400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:177580200-177581400	Active TSS	Esophagus	oesophagus
48	chr5:177580200-177581400	Active TSS	Gastric	stomach
49	chr5:177580200-177581400	Active TSS	Left Ventricle	heart
50	chr5:177580200-177581400	Active TSS	Ovary	ovary

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