Variant report

Variant	rs7717640
Chromosome Location	chr5:107006644-107006645
allele	A/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	MAX	chr5:107006020-107006929	MCF-7	breast:	n/a	chr5:107006621-107006631
2	POLR2A	chr5:107006531-107006882	A549	lung:	n/a	n/a
3	SIN3A	chr5:107004143-107009658	H1-hESC	embryonic stem cell:	n/a	chr5:107006662-107006673 chr5:107007128-107007141 chr5:107008731-107008740 chr5:107006059-107006068 chr5:107007404-107007415 chr5:107007253-107007266
4	POLR2A	chr5:107006462-107008238	GM12878	blood:	n/a	n/a
5	POLR2A	chr5:107006446-107006713	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr5:107004197-107007511	H1-neurons	neurons:	n/a	n/a
7	E2F6	chr5:107006540-107008733	H1-hESC	embryonic stem cell:	n/a	chr5:107007775-107007782 chr5:107006894-107006901 chr5:107007250-107007260 chr5:107007775-107007782 chr5:107007774-107007783 chr5:107006659-107006669 chr5:107006656-107006666 chr5:107007771-107007783 chr5:107007775-107007782 chr5:107006893-107006901
8	POLR2A	chr5:107005737-107007010	H1-neurons	neurons:	n/a	n/a
9	MAX	chr5:107005867-107009014	HCT-116	colon:	n/a	chr5:107008043-107008052 chr5:107006621-107006631 chr5:107007511-107007518 chr5:107008046-107008056
10	MAX	chr5:107005041-107009765	A549	lung:	n/a	chr5:107008043-107008052 chr5:107006621-107006631 chr5:107007511-107007518 chr5:107008046-107008056
11	MYC	chr5:107005922-107009065	A549	lung:	n/a	chr5:107008043-107008052 chr5:107006621-107006631 chr5:107007511-107007518 chr5:107008046-107008056
12	POLR2A	chr5:107006555-107006968	A549	lung:	n/a	n/a
13	SMARCB1	chr5:107005120-107008256	Hela-S3	cervix:	n/a	n/a
14	MAX	chr5:107005286-107008387	SK-N-SH	brain:	n/a	chr5:107008043-107008052 chr5:107006621-107006631 chr5:107007511-107007518 chr5:107008046-107008056
15	MAX	chr5:107006626-107008969	SK-N-SH	brain:	n/a	chr5:107008043-107008052 chr5:107007511-107007518 chr5:107008046-107008056
16	HA-E2F1	chr5:107005127-107009710	MCF-7	breast:	n/a	chr5:107007775-107007782 chr5:107005769-107005777 chr5:107006894-107006901 chr5:107006120-107006130 chr5:107007250-107007260 chr5:107006119-107006128 chr5:107007775-107007782 chr5:107007774-107007783 chr5:107005379-107005393 chr5:107006659-107006669 chr5:107009059-107009068 chr5:107005382-107005396 chr5:107006656-107006666 chr5:107007771-107007783 chr5:107007775-107007782 chr5:107005769-107005777 chr5:107006034-107006046 chr5:107005769-107005776 chr5:107006089-107006098
17	POLR2A	chr5:107006481-107006941	A549	lung:	n/a	n/a
18	MXI1	chr5:107005903-107009840	IMR90	lung:	n/a	chr5:107008192-107008201 chr5:107008504-107008513 chr5:107006889-107006904
19	CTBP2	chr5:107005023-107009734	H1-hESC	embryonic stem cell:	n/a	n/a
20	MXI1	chr5:107005703-107009654	GM12878	blood:	n/a	chr5:107008192-107008201 chr5:107008504-107008513 chr5:107006889-107006904
21	ZNF263	chr5:107006585-107009759	HEK293-T-REx	kidney:	n/a	chr5:107007686-107007707
22	POLR2A	chr5:107005295-107009089	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr5:107006552-107007242	MCF-7	breast:	n/a	n/a
24	MAZ	chr5:107005857-107009762	IMR90	lung:	n/a	chr5:107008043-107008052 chr5:107006621-107006631 chr5:107007511-107007518 chr5:107008046-107008056
25	POLR2A	chr5:107006112-107009810	MCF10A-Er-Src	breast:	n/a	n/a
26	TCF7L2	chr5:107006614-107008779	HCT-116	colon:	n/a	n/a
27	JUND	chr5:107006413-107006951	A549	lung:	n/a	n/a
28	RAD21	chr5:107003937-107010170	SK-N-SH	brain:	n/a	chr5:107007238-107007250 chr5:107006656-107006670
29	POLR2A	chr5:107006541-107007137	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr5:107006518-107007829	A549	lung:	n/a	n/a
31	CHD2	chr5:107005998-107008748	Hela-S3	cervix:	n/a	n/a
32	BHLHE40	chr5:107005925-107006657	GM12878	blood:	n/a	n/a
33	SIN3AK20	chr5:107004613-107008882	PANC-1	pancreas:	n/a	n/a
34	POLR2A	chr5:107006615-107007169	HUVEC	blood vessel:	n/a	n/a
35	MAX	chr5:107005870-107009842	HCT-116	colon:	n/a	chr5:107008043-107008052 chr5:107006621-107006631 chr5:107007511-107007518 chr5:107008046-107008056
36	MXI1	chr5:107003908-107009975	SK-N-SH	brain:	n/a	chr5:107008192-107008201 chr5:107008504-107008513 chr5:107006889-107006904
37	CREB1	chr5:107006545-107007003	A549	lung:	n/a	n/a
38	POLR2A	chr5:107006051-107008237	GM12878	blood:	n/a	n/a
39	MAX	chr5:107006021-107009728	MCF-7	breast:	n/a	chr5:107008043-107008052 chr5:107006621-107006631 chr5:107007511-107007518 chr5:107008046-107008056
40	MYC	chr5:107006489-107007005	MCF-7	breast:	n/a	chr5:107006621-107006631
41	CHD2	chr5:107006538-107006934	GM12878	blood:	n/a	n/a
42	POLR2A	chr5:107006083-107008745	ECC-1	luminal epithelium:	n/a	n/a
43	CHD1	chr5:107006597-107007367	GM12878	blood:	n/a	n/a
44	POLR2A	chr5:107005128-107009658	Hela-S3	cervix:	n/a	n/a
45	BCLAF1	chr5:107006633-107007344	GM12878	blood:	n/a	chr5:107006655-107006668 chr5:107006656-107006665 chr5:107006768-107006781 chr5:107006657-107006670 chr5:107006771-107006784
46	MAX	chr5:107005289-107009726	Hela-S3	cervix:	n/a	chr5:107008043-107008052 chr5:107006621-107006631 chr5:107007511-107007518 chr5:107008046-107008056
47	MAX	chr5:107004764-107009849	A549	lung:	n/a	chr5:107008043-107008052 chr5:107004981-107004991 chr5:107006621-107006631 chr5:107007511-107007518 chr5:107008046-107008056
48	GATA3	chr5:107005874-107008960	A549	lung:	n/a	chr5:107008275-107008284 chr5:107008921-107008931 chr5:107006176-107006185 chr5:107008389-107008402
49	POLR2A	chr5:107006609-107008654	GM18951	blood:	n/a	n/a
50	MAX	chr5:107006041-107009699	ECC-1	luminal epithelium:	n/a	chr5:107008043-107008052 chr5:107006621-107006631 chr5:107007511-107007518 chr5:107008046-107008056

Variant related genes	Relation type
EFNA5	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10055714	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10076353	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11242644	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12657154	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13159331	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13184509	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1572255	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17351315	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34685651	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4957707	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56215442	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62357892	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62357896	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7705512	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7707690	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7721633	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7723130	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7732784	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs897413	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34018	chr5:106720912-107110506	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107000000-107006800	Active TSS	GM12878-XiMat	blood
2	chr5:107002400-107009600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:107002400-107009800	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr5:107003000-107009600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:107003000-107009600	Active TSS	A549	lung
6	chr5:107003200-107009600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:107003800-107009600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:107003800-107009600	Active TSS	NHDF-Ad	bronchial
9	chr5:107004000-107008600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:107004000-107008600	Active TSS	HSMM	muscle
11	chr5:107004000-107009000	Active TSS	Left Ventricle	heart
12	chr5:107004000-107009400	Active TSS	Placenta Amnion	Placenta Amnion
13	chr5:107004000-107009600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:107004000-107009600	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr5:107004000-107009600	Active TSS	Aorta	Aorta
16	chr5:107004000-107009600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
17	chr5:107004000-107009600	Active TSS	Right Atrium	heart
18	chr5:107004200-107009400	Active TSS	NHLF	lung
19	chr5:107004200-107009600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:107004200-107009600	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr5:107004200-107009600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr5:107004400-107007600	Active TSS	NH-A	brain
23	chr5:107004400-107009600	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr5:107004400-107009600	Active TSS	Brain Anterior Caudate	brain
25	chr5:107004400-107009600	Active TSS	Rectal Smooth Muscle	rectum
26	chr5:107004600-107007000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
27	chr5:107004600-107007000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
28	chr5:107004600-107007600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
29	chr5:107004600-107007800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
30	chr5:107004600-107008600	Active TSS	HMEC	breast
31	chr5:107004600-107008600	Active TSS	NHEK	skin
32	chr5:107004600-107009000	Active TSS	Rectal Mucosa Donor 31	rectum
33	chr5:107004600-107009400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr5:107004600-107009400	Active TSS	Gastric	stomach
35	chr5:107004600-107009600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr5:107004600-107009600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr5:107004600-107009600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:107004600-107009600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr5:107004600-107009600	Active TSS	Fetal Kidney	kidney
40	chr5:107004600-107009600	Active TSS	Fetal Lung	lung
41	chr5:107004600-107009600	Active TSS	Stomach Mucosa	stomach
42	chr5:107004800-107007000	Active TSS	Duodenum Mucosa	Duodenum
43	chr5:107004800-107007200	Active TSS	Hela-S3	cervix
44	chr5:107004800-107008800	Active TSS	Muscle Satellite Cultured Cells	--
45	chr5:107004800-107009400	Active TSS	Ovary	ovary
46	chr5:107004800-107009600	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr5:107004800-107009600	Active TSS	Esophagus	oesophagus
48	chr5:107005000-107006800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
49	chr5:107005000-107007200	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr5:107005000-107009600	Active TSS	HUES48 Cell Line	embryonic stem cell

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