Variant report

Variant	rs10039900
Chromosome Location	chr5:127874340-127874341
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	POLR2A	chr5:127873698-127875045	A549	lung:	n/a	n/a
2	POLR2A	chr5:127873300-127874665	HUVEC	blood vessel:	n/a	n/a
3	TCF12	chr5:127873142-127874965	A549	lung:	n/a	chr5:127874714-127874722
4	POLR2A	chr5:127873540-127874599	HUVEC	blood vessel:	n/a	n/a
5	TAF1	chr5:127872851-127874735	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr5:127873069-127874650	ProgFib	skin:	n/a	n/a
7	EGR1	chr5:127873912-127874598	H1-hESC	embryonic stem cell:	n/a	chr5:127874280-127874293 chr5:127873942-127873952
8	POLR2A	chr5:127873627-127874604	HUVEC	blood vessel:	n/a	n/a
9	MAZ	chr5:127872770-127875254	IMR90	lung:	n/a	chr5:127874030-127874039
10	POLR2A	chr5:127874104-127875124	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr5:127873630-127874594	HUVEC	blood vessel:	n/a	n/a
12	TBP	chr5:127873148-127875197	H1-hESC	embryonic stem cell:	n/a	n/a
13	SPI1	chr5:127873876-127874602	HL-60	blood:	n/a	chr5:127874514-127874527
14	MYC	chr5:127873499-127874592	MCF10A-Er-Src	breast:	n/a	chr5:127874030-127874039
15	PBX3	chr5:127873923-127874348	A549	lung:	n/a	n/a
16	CEBPB	chr5:127874329-127874580	H1-hESC	embryonic stem cell:	n/a	n/a
17	JUND	chr5:127874172-127874698	H1-hESC	embryonic stem cell:	n/a	chr5:127874362-127874371
18	POLR2A	chr5:127873632-127875183	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr5:127872912-127875135	NB4	blood:	n/a	chr5:127874030-127874039
20	RAD21	chr5:127874283-127874951	IMR90	lung:	n/a	n/a
21	E2F6	chr5:127872896-127874462	A549	lung:	n/a	chr5:127872971-127872982 chr5:127874013-127874022 chr5:127872975-127872982
22	ZBTB7A	chr5:127873821-127875102	ECC-1	luminal epithelium:	n/a	chr5:127874012-127874021 chr5:127874376-127874385
23	E2F4	chr5:127873287-127874432	MCF10A-Er-Src	breast:	n/a	chr5:127874013-127874022
24	STAT3	chr5:127874296-127874559	MCF10A-Er-Src	breast:	n/a	chr5:127874514-127874526
25	SP1	chr5:127873646-127875086	A549	lung:	n/a	chr5:127874513-127874527 chr5:127874348-127874359 chr5:127874518-127874532 chr5:127874345-127874359 chr5:127874405-127874426 chr5:127874519-127874528
26	POLR2A	chr5:127873123-127874777	NB4	blood:	n/a	n/a
27	MAX	chr5:127873879-127874496	A549	lung:	n/a	chr5:127874030-127874039
28	STAT3	chr5:127874296-127874524	MCF10A-Er-Src	breast:	n/a	n/a
29	TCF12	chr5:127874224-127874653	H1-hESC	embryonic stem cell:	n/a	n/a
30	KAP1	chr5:127874143-127874503	U2OS	brain:	n/a	n/a
31	POLR2A	chr5:127874333-127874752	A549	lung:	n/a	n/a
32	POLR2A	chr5:127872030-127875377	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr5:127873347-127874984	HUVEC	blood vessel:	n/a	n/a
34	SP1	chr5:127873718-127874937	A549	lung:	n/a	chr5:127874513-127874527 chr5:127874348-127874359 chr5:127874518-127874532 chr5:127874345-127874359 chr5:127874405-127874426 chr5:127874519-127874528
35	RCOR1	chr5:127871794-127875413	IMR90	lung:	n/a	n/a
36	CREB1	chr5:127873712-127874982	A549	lung:	n/a	n/a
37	TAF1	chr5:127872976-127874506	ECC-1	luminal epithelium:	n/a	n/a
38	EP300	chr5:127873565-127874476	ECC-1	luminal epithelium:	n/a	n/a
39	RAD21	chr5:127874146-127875272	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAX	chr5:127872216-127874746	H1-hESC	embryonic stem cell:	n/a	chr5:127874030-127874039
41	POLR2A	chr5:127873593-127874609	A549	lung:	n/a	n/a
42	CTBP2	chr5:127871959-127875032	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr5:127873638-127874412	ECC-1	luminal epithelium:	n/a	n/a
44	MYC	chr5:127873884-127874398	MCF10A-Er-Src	breast:	n/a	chr5:127874030-127874039
45	MYC	chr5:127873079-127875173	NB4	blood:	n/a	chr5:127874030-127874039
46	FOS	chr5:127874177-127874353	MCF10A-Er-Src	breast:	n/a	n/a
47	NANOG	chr5:127874196-127874627	H1-hESC	embryonic stem cell:	n/a	n/a
48	KAP1	chr5:127874312-127875334	HEK293	kidney:	n/a	n/a
49	CHD2	chr5:127874123-127874655	H1-hESC	embryonic stem cell:	n/a	chr5:127874378-127874388
50	MXI1	chr5:127874000-127874657	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
FBN2	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10040056	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10042096	0.84[ASN][1000 genomes]
rs10053025	0.84[ASN][1000 genomes]
rs10062344	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10063362	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10063961	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10477685	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10478812	0.80[ASN][1000 genomes]
rs10478813	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10478814	0.84[ASN][1000 genomes]
rs11960575	0.80[ASN][1000 genomes]
rs17164094	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17164113	0.84[ASN][1000 genomes]
rs1897998	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55721088	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55735252	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56049336	0.80[ASN][1000 genomes]
rs57050667	0.84[ASN][1000 genomes]
rs58889726	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59674940	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60201468	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60571728	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60975118	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6595830	0.84[ASN][1000 genomes]
rs6595831	0.84[ASN][1000 genomes]
rs6595834	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6595836	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6595837	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6595841	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6595842	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6860199	0.84[ASN][1000 genomes]
rs6864057	0.87[ASN][1000 genomes]
rs6886186	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6887851	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6892484	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6893116	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6893181	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6893248	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6893301	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73346331	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73784600	0.81[ASN][1000 genomes]
rs73787623	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73787627	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs768744	0.83[ASN][1000 genomes]
rs7703313	0.80[ASN][1000 genomes]
rs7708713	0.84[ASN][1000 genomes]
rs7713044	0.84[ASN][1000 genomes]
rs7722917	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7722950	0.84[ASN][1000 genomes]
rs7723500	0.84[ASN][1000 genomes]
rs7725740	0.84[ASN][1000 genomes]
rs7726535	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9327478	0.83[EUR][1000 genomes];0.84[ASN][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	nsv531991	chr5:127624564-127966085	Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	esv2763497	chr5:127745955-127882468	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv530822	chr5:127777365-127900742	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv427734	chr5:127805281-128088632	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127869200-127875000	Active TSS	Fetal Heart	heart
2	chr5:127870800-127875200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr5:127871000-127875400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr5:127871200-127875400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr5:127871600-127875000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
6	chr5:127871800-127874400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
7	chr5:127871800-127874800	Bivalent/Poised TSS	NHDF-Ad	bronchial
8	chr5:127871800-127875200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:127871800-127875200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
10	chr5:127871800-127875200	Active TSS	Left Ventricle	heart
11	chr5:127871800-127875200	Active TSS	Right Ventricle	heart
12	chr5:127871800-127875400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr5:127872000-127874400	Bivalent/Poised TSS	Fetal Brain Female	brain
14	chr5:127872000-127875200	Bivalent/Poised TSS	Fetal Stomach	stomach
15	chr5:127872000-127875400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:127872200-127874600	Active TSS	A549	lung
17	chr5:127872200-127875000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:127872200-127875200	Active TSS	Right Atrium	heart
19	chr5:127872200-127875400	Active TSS	Muscle Satellite Cultured Cells	--
20	chr5:127872200-127875400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:127872400-127874400	Bivalent/Poised TSS	Brain Angular Gyrus	brain
22	chr5:127872400-127874400	Active TSS	Osteobl	bone
23	chr5:127872400-127874600	Active TSS	NHEK	skin
24	chr5:127872400-127875000	Active TSS	Ovary	ovary
25	chr5:127872400-127875400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr5:127872400-127875400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr5:127872600-127874600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr5:127872600-127874600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:127872600-127874600	Active TSS	Fetal Lung	lung
30	chr5:127872600-127874600	Active TSS	Hela-S3	cervix
31	chr5:127872600-127874600	Active TSS	NH-A	brain
32	chr5:127872600-127874800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
33	chr5:127872600-127875000	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:127872600-127875000	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr5:127872600-127875200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:127872600-127875200	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
37	chr5:127872600-127875200	Active TSS	Placenta Amnion	Placenta Amnion
38	chr5:127872600-127875400	Active TSS	Fetal Kidney	kidney
39	chr5:127872800-127874400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr5:127872800-127874400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:127872800-127874600	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr5:127872800-127874600	Bivalent/Poised TSS	Thymus	Thymus
43	chr5:127872800-127874800	Active TSS	Aorta	Aorta
44	chr5:127872800-127875000	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr5:127872800-127875000	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr5:127872800-127875200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr5:127872800-127875200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr5:127872800-127875200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
49	chr5:127872800-127875200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
50	chr5:127872800-127875200	Active TSS	NHLF	lung

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