Variant report

Variant	rs73389259
Chromosome Location	chr7:39742947-39742948
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	CTCF	chr7:39742880-39743030	AG04449	skin:	n/a	chr7:39742930-39742939
2	CTCF	chr7:39742880-39743030	HRPEpiC	eye:	n/a	chr7:39742930-39742939
3	CTCF	chr7:39742880-39743030	HPAF	blood vessel:	n/a	chr7:39742930-39742939
4	CTCF	chr7:39742800-39742950	NHDF-neo	bronchial:	n/a	chr7:39742930-39742939
5	CTCF	chr7:39742880-39743030	NHEK	skin:	n/a	chr7:39742930-39742939
6	CTCF	chr7:39742880-39743030	RPTEC	kidney:	n/a	chr7:39742930-39742939
7	CTCF	chr7:39742800-39742950	HPF	lung:	n/a	chr7:39742930-39742939
8	CEBPB	chr7:39742820-39743094	IMR90	lung:	n/a	n/a
9	CTCF	chr7:39742860-39743010	HCFaa	heart:	n/a	chr7:39742930-39742939
10	EBF1	chr7:39742779-39743089	GM12878	blood:	n/a	chr7:39742907-39742917 chr7:39742907-39742916 chr7:39742905-39742918
11	CREB1	chr7:39742704-39743177	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr7:39742900-39743050	HMF	breast:	n/a	chr7:39742930-39742939
13	EBF1	chr7:39742741-39743079	GM12878	blood:	n/a	chr7:39742907-39742917 chr7:39742907-39742916 chr7:39742905-39742918
14	CTCF	chr7:39742900-39743050	AG04450	lung:	n/a	chr7:39742930-39742939
15	CTCF	chr7:39742800-39742950	NHLF	lung:	n/a	chr7:39742930-39742939
16	CTCF	chr7:39742840-39742990	AG09309	skin:	n/a	chr7:39742930-39742939
17	CTCF	chr7:39742900-39743050	AG09319	gingival:	n/a	chr7:39742930-39742939
18	CTCF	chr7:39742840-39742990	AG10803	skin:	n/a	chr7:39742930-39742939
19	CTCF	chr7:39742800-39742950	HVMF	connective:	n/a	chr7:39742930-39742939
20	CTCF	chr7:39742840-39742990	HMEC	breast:	n/a	chr7:39742930-39742939
21	CTCF	chr7:39742900-39743050	HCPEpiC	choroid plexus:	n/a	chr7:39742930-39742939
22	CTCF	chr7:39742880-39743030	HVMF	connective:	n/a	chr7:39742930-39742939
23	CTCF	chr7:39742917-39742988	Gliobla	brain:	n/a	chr7:39742930-39742939
24	CTCF	chr7:39742880-39743030	HEEpiC	esophagus:	n/a	chr7:39742930-39742939
25	CTCF	chr7:39742860-39743010	HRPEpiC	eye:	n/a	chr7:39742930-39742939
26	CTCF	chr7:39742800-39742950	SAEC	small airway:	n/a	chr7:39742930-39742939
27	CTCF	chr7:39742868-39743010	MCF-7	breast:	n/a	chr7:39742930-39742939
28	CTCF	chr7:39742800-39743070	NB4	blood:	n/a	chr7:39742930-39742939
29	CTCF	chr7:39742880-39743030	BE2_C	brain:	n/a	chr7:39742930-39742939
30	CTCF	chr7:39742900-39743050	GM12866	blood:	n/a	chr7:39742930-39742939
31	CTCF	chr7:39742860-39743010	Hela-S3	cervix:	n/a	chr7:39742930-39742939
32	CTCF	chr7:39742840-39742990	HepG2	liver:	n/a	chr7:39742930-39742939
33	CTCF	chr7:39742900-39743050	NHDF-neo	bronchial:	n/a	chr7:39742930-39742939
34	CTCF	chr7:39742860-39743010	Caco-2	colon:	n/a	chr7:39742930-39742939
35	EBF1	chr7:39742835-39743091	GM12878	blood:	n/a	chr7:39742907-39742917 chr7:39742907-39742916 chr7:39742905-39742918
36	CTCF	chr7:39742900-39743050	HAc	cerebellar:	n/a	chr7:39742930-39742939
37	CTCF	chr7:39742880-39743030	K562	blood:	n/a	chr7:39742930-39742939
38	CTCF	chr7:39742880-39743047	Hela-S3	cervix:	n/a	chr7:39742930-39742939
39	CTCF	chr7:39742860-39743010	MCF-7	breast:	n/a	chr7:39742930-39742939
40	CTCF	chr7:39742840-39742990	HPF	lung:	n/a	chr7:39742930-39742939
41	CTCF	chr7:39742870-39743037	K562	blood:	n/a	chr7:39742930-39742939
42	CTCF	chr7:39742840-39742990	HCPEpiC	choroid plexus:	n/a	chr7:39742930-39742939
43	CTCF	chr7:39742860-39743010	SK-N-SH_RA	brain:	n/a	chr7:39742930-39742939
44	CTCF	chr7:39742840-39742990	AoAF	blood vessel:	n/a	chr7:39742930-39742939
45	CTCF	chr7:39742800-39742950	A549	lung:	n/a	chr7:39742930-39742939
46	CTCF	chr7:39742800-39742950	BJ	skin:	n/a	chr7:39742930-39742939
47	CTCF	chr7:39742880-39743030	WERI-Rb-1	eye:	n/a	chr7:39742930-39742939
48	CTCF	chr7:39742860-39743010	HA-sp	spinal cord:	n/a	chr7:39742930-39742939
49	CTCF	chr7:39742820-39742970	HRE	kidney:	n/a	chr7:39742930-39742939
50	CTCF	chr7:39742860-39743010	HUVEC	blood vessel:	n/a	chr7:39742930-39742939

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:39739429..39741292-chr7:39741440..39743225,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228554	TF binding region
ENSG00000006451	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs17171616	0.88[AFR][1000 genomes]
rs3801265	0.84[AFR][1000 genomes]
rs57509649	0.96[AFR][1000 genomes]
rs59341821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73381116	0.96[AFR][1000 genomes]
rs73381118	0.96[AFR][1000 genomes]
rs73381122	0.84[AFR][1000 genomes]
rs73381129	0.86[AFR][1000 genomes]
rs73381131	0.96[AFR][1000 genomes]
rs73387331	0.96[AFR][1000 genomes]
rs73387334	0.93[AFR][1000 genomes]
rs73387337	0.96[AFR][1000 genomes]
rs73387350	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73387354	0.88[AFR][1000 genomes]
rs73387357	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73387375	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73389244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73389280	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	nsv508451	chr7:39660784-39787222	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv887971	chr7:39662268-39745775	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv427777	chr7:39726513-39936904	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39715200-39749400	Weak transcription	Aorta	Aorta
2	chr7:39723800-39743000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:39727400-39747800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr7:39730600-39749200	Weak transcription	Ovary	ovary
5	chr7:39732000-39748000	Strong transcription	HUVEC	blood vessel
6	chr7:39732000-39749200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr7:39734200-39746200	Weak transcription	Fetal Kidney	kidney
8	chr7:39734600-39743000	Strong transcription	HSMM	muscle
9	chr7:39735600-39743200	Strong transcription	Primary B cells from cord blood	blood
10	chr7:39735600-39743400	Strong transcription	Primary T cells from cord blood	blood
11	chr7:39736000-39743600	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr7:39736600-39749400	Weak transcription	Fetal Heart	heart
13	chr7:39737200-39743000	Weak transcription	Brain Hippocampus Middle	brain
14	chr7:39737400-39743800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr7:39737400-39749800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr7:39737600-39743200	Strong transcription	NHDF-Ad	bronchial
17	chr7:39737600-39748800	Weak transcription	Colon Smooth Muscle	Colon
18	chr7:39737800-39749400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr7:39737800-39749400	Weak transcription	Psoas Muscle	Psoas
20	chr7:39738000-39748600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:39738000-39749200	Weak transcription	Fetal Brain Female	brain
22	chr7:39738000-39749400	Weak transcription	Placenta	Placenta
23	chr7:39738400-39743600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr7:39738400-39744400	Weak transcription	HepG2	liver
25	chr7:39738400-39748400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr7:39738600-39744600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr7:39738600-39748800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr7:39738600-39748800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr7:39738600-39749200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr7:39739600-39743000	Weak transcription	K562	blood
31	chr7:39739600-39749600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr7:39740000-39743200	Enhancers	Stomach Mucosa	stomach
33	chr7:39740200-39744800	Weak transcription	Brain Substantia Nigra	brain
34	chr7:39740200-39746200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr7:39740200-39747200	Weak transcription	Gastric	stomach
36	chr7:39740200-39748000	Weak transcription	Primary B cells from peripheral blood	blood
37	chr7:39740200-39749200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr7:39740200-39749400	Weak transcription	Pancreas	Pancrea
39	chr7:39740200-39749400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr7:39740200-39749600	Weak transcription	Lung	lung
41	chr7:39740200-39752000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr7:39740400-39745000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr7:39740400-39745600	Weak transcription	Esophagus	oesophagus
44	chr7:39740400-39747400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr7:39740400-39749000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr7:39740400-39749600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr7:39740600-39743800	Weak transcription	A549	lung
48	chr7:39740600-39748200	Weak transcription	Brain Anterior Caudate	brain
49	chr7:39740600-39749400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr7:39740600-39749400	Weak transcription	Rectal Mucosa Donor 29	rectum

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