Variant report

Variant	rs55905016
Chromosome Location	chr2:47716086-47716087
allele	C/T
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	MYC	chr2:47715971-47716348	MCF10A-Er-Src	breast:	n/a	chr2:47716133-47716142 chr2:47716131-47716141
2	POLR2A	chr2:47715578-47717391	K562	blood:	n/a	n/a
3	POLR2A	chr2:47715883-47716670	MCF-7	breast:	n/a	n/a
4	USF1	chr2:47715992-47716219	SK-N-SH_RA	brain:	n/a	n/a
5	FOS	chr2:47716033-47716509	HUVEC	blood vessel:	n/a	n/a
6	NFIC	chr2:47715971-47716572	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr2:47715990-47716486	H1-hESC	embryonic stem cell:	n/a	n/a
8	FOS	chr2:47716064-47716540	MCF10A-Er-Src	breast:	n/a	n/a
9	CEBPB	chr2:47715968-47716597	A549	lung:	n/a	chr2:47716044-47716056 chr2:47716338-47716349
10	POLR2A	chr2:47716026-47716654	K562	blood:	n/a	n/a
11	FOSL2	chr2:47715943-47716622	SK-N-SH	brain:	n/a	n/a
12	GATA2	chr2:47715804-47716130	SH-SY5Y	brain:	n/a	n/a
13	MYC	chr2:47715901-47716496	MCF10A-Er-Src	breast:	n/a	chr2:47716133-47716142 chr2:47716131-47716141
14	MAX	chr2:47715822-47716582	A549	lung:	n/a	chr2:47716133-47716142 chr2:47716131-47716141
15	JUND	chr2:47716062-47716414	A549	lung:	n/a	n/a
16	FOSL2	chr2:47715867-47716470	A549	lung:	n/a	n/a
17	TCF12	chr2:47715805-47716607	SK-N-SH	brain:	n/a	chr2:47716151-47716158
18	CEBPB	chr2:47716032-47716499	A549	lung:	n/a	chr2:47716044-47716056 chr2:47716338-47716349
19	TCF12	chr2:47715896-47716501	A549	lung:	n/a	chr2:47716151-47716158
20	FOS	chr2:47716080-47716450	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr2:47716004-47716436	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr2:47715927-47716699	PANC-1	pancreas:	n/a	n/a
23	USF1	chr2:47715938-47716366	A549	lung:	n/a	n/a
24	USF1	chr2:47715926-47716392	A549	lung:	n/a	n/a
25	GATA3	chr2:47715742-47716305	MCF-7	breast:	n/a	n/a
26	FOSL2	chr2:47716045-47716375	A549	lung:	n/a	n/a
27	POLR2A	chr2:47715755-47716800	H1-hESC	embryonic stem cell:	n/a	n/a
28	USF1	chr2:47715960-47716357	A549	lung:	n/a	n/a
29	STAT3	chr2:47716045-47716367	MCF10A-Er-Src	breast:	n/a	n/a
30	NFIC	chr2:47715972-47716509	ECC-1	luminal epithelium:	n/a	n/a
31	NFIC	chr2:47715879-47716633	SK-N-SH	brain:	n/a	n/a
32	FOS	chr2:47716080-47716436	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr2:47716014-47716305	H1-hESC	embryonic stem cell:	n/a	n/a
34	BACH1	chr2:47716053-47716135	H1-hESC	embryonic stem cell:	n/a	n/a
35	JUND	chr2:47715847-47716542	SK-N-SH	brain:	n/a	n/a
36	PRDM1	chr2:47716059-47716363	Hela-S3	cervix:	n/a	chr2:47716196-47716211
37	USF1	chr2:47715957-47716236	A549	lung:	n/a	n/a
38	MAX	chr2:47715918-47716375	MCF-7	breast:	n/a	chr2:47716133-47716142 chr2:47716131-47716141
39	MAX	chr2:47715886-47716506	A549	lung:	n/a	chr2:47716133-47716142 chr2:47716131-47716141
40	MAX	chr2:47715932-47716355	ECC-1	luminal epithelium:	n/a	chr2:47716133-47716142 chr2:47716131-47716141
41	POLR2A	chr2:47716047-47716245	H1-hESC	embryonic stem cell:	n/a	n/a
42	FOXA2	chr2:47716082-47716477	A549	lung:	n/a	n/a
43	GATA3	chr2:47715654-47716509	SK-N-SH	brain:	n/a	n/a
44	USF1	chr2:47716038-47716278	SK-N-SH_RA	brain:	n/a	n/a
45	MAX	chr2:47715943-47716453	ECC-1	luminal epithelium:	n/a	chr2:47716133-47716142 chr2:47716131-47716141
46	POLR2A	chr2:47715840-47716330	Hela-S3	cervix:	n/a	n/a
47	USF1	chr2:47715987-47716316	A549	lung:	n/a	n/a
48	POLR2A	chr2:47716054-47716569	PANC-1	pancreas:	n/a	n/a

Variant related genes	Relation type
ENSG00000236558	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs17036586	1.00[AMR][1000 genomes]
rs17036616	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17036622	0.80[AFR][1000 genomes]
rs17039236	1.00[AMR][1000 genomes]
rs17217849	1.00[AMR][1000 genomes]
rs17217961	1.00[AMR][1000 genomes]
rs17218648	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17224122	1.00[AMR][1000 genomes]
rs17224724	1.00[AMR][1000 genomes]
rs17224738	1.00[AMR][1000 genomes]
rs17224815	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1800151	1.00[AMR][1000 genomes]
rs55815447	1.00[AMR][1000 genomes]
rs56076616	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56958162	1.00[AMR][1000 genomes]
rs56983268	1.00[AMR][1000 genomes]
rs57972954	1.00[AMR][1000 genomes]
rs58012164	1.00[AMR][1000 genomes]
rs58080795	1.00[AMR][1000 genomes]
rs58930161	1.00[AMR][1000 genomes]
rs59974084	1.00[AMR][1000 genomes]
rs60121180	1.00[AMR][1000 genomes]
rs60512750	1.00[AMR][1000 genomes]
rs61282650	1.00[AMR][1000 genomes]
rs61635665	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72882725	1.00[AMR][1000 genomes]
rs72882752	1.00[AMR][1000 genomes]
rs72882765	1.00[AMR][1000 genomes]
rs72882783	1.00[AMR][1000 genomes]
rs72882786	1.00[AMR][1000 genomes]
rs72882796	1.00[AMR][1000 genomes]
rs72882802	1.00[AMR][1000 genomes]
rs72884625	1.00[AMR][1000 genomes]
rs72884632	1.00[AMR][1000 genomes]
rs72884676	1.00[AMR][1000 genomes]
rs72886304	1.00[AMR][1000 genomes]
rs72886358	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72888237	1.00[AMR][1000 genomes]
rs72888238	1.00[AMR][1000 genomes]
rs72888263	1.00[AMR][1000 genomes]
rs73927801	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73927802	1.00[AMR][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	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47658200-47724800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:47693600-47716800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:47697000-47716200	Weak transcription	Fetal Brain Female	brain
4	chr2:47702800-47727000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:47703800-47722000	Weak transcription	Brain Hippocampus Middle	brain
6	chr2:47704200-47716200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:47705800-47717000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:47706200-47716200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:47706600-47716200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:47710000-47716200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:47712000-47716200	Weak transcription	Fetal Stomach	stomach
12	chr2:47712200-47716400	Weak transcription	Fetal Intestine Large	intestine
13	chr2:47712200-47716400	Weak transcription	Left Ventricle	heart
14	chr2:47712600-47716400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:47712600-47716400	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:47712600-47716600	Weak transcription	HepG2	liver
17	chr2:47712800-47716200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:47712800-47716400	Weak transcription	Hela-S3	cervix
19	chr2:47712800-47721800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:47713000-47716200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr2:47713000-47716200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:47713000-47716400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:47713000-47717400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:47713000-47717600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:47713200-47716400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr2:47713400-47716800	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr2:47713600-47718200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:47714400-47716200	Enhancers	Stomach Mucosa	stomach
29	chr2:47714400-47717800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:47714600-47727200	Weak transcription	Primary T cells from cord blood	blood
31	chr2:47715000-47716200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr2:47715000-47716400	Weak transcription	HSMMtube	muscle
33	chr2:47715000-47716800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:47715000-47717000	Weak transcription	Dnd41	blood
35	chr2:47715000-47721800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr2:47715400-47716200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:47715400-47717400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:47715400-47718000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:47715600-47716200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:47715600-47716600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:47715600-47716600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:47715600-47716600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:47715600-47718000	Enhancers	NHEK	skin
44	chr2:47715600-47718200	Enhancers	HMEC	breast
45	chr2:47715800-47716600	Enhancers	HUVEC	blood vessel
46	chr2:47715800-47716600	Enhancers	NHDF-Ad	bronchial
47	chr2:47715800-47716600	Enhancers	Osteobl	bone
48	chr2:47715800-47716800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:47715800-47716800	Enhancers	NH-A	brain
50	chr2:47715800-47717000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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