Variant report

Variant	rs555098658
Chromosome Location	chr7:39989728-39989729
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	RELA	chr7:39988693-39990191	GM19099	blood:	n/a	n/a
2	ELF1	chr7:39988502-39990278	K562	blood:	n/a	chr7:39989855-39989864 chr7:39989461-39989473 chr7:39989457-39989466 chr7:39989460-39989469 chr7:39989854-39989865 chr7:39989466-39989475 chr7:39989854-39989865 chr7:39990120-39990132 chr7:39989463-39989472 chr7:39990213-39990225 chr7:39989458-39989470
3	USF2	chr7:39989660-39990037	GM12878	blood:	n/a	n/a
4	TRIM28	chr7:39988580-39989963	K562	blood:	n/a	chr7:39989206-39989214
5	EP300	chr7:39988999-39991304	ECC-1	luminal epithelium:	n/a	chr7:39989388-39989404 chr7:39989784-39989797 chr7:39989476-39989490 chr7:39989462-39989471 chr7:39990215-39990231 chr7:39989452-39989468 chr7:39989459-39989468 chr7:39989454-39989470 chr7:39989465-39989474 chr7:39989108-39989115
6	SP1	chr7:39988688-39990025	A549	lung:	n/a	chr7:39989526-39989540 chr7:39989360-39989374 chr7:39989333-39989347 chr7:39989792-39989801 chr7:39989901-39989911 chr7:39989354-39989368 chr7:39989416-39989430 chr7:39989168-39989179 chr7:39989281-39989295 chr7:39989902-39989911
7	BATF	chr7:39989596-39989936	GM12878	blood:	n/a	n/a
8	MYC	chr7:39988576-39990092	K562	blood:	n/a	chr7:39989183-39989193 chr7:39989411-39989421
9	NR2F2	chr7:39989574-39990064	K562	blood:	n/a	n/a
10	SP1	chr7:39988635-39990063	A549	lung:	n/a	chr7:39989526-39989540 chr7:39989360-39989374 chr7:39989333-39989347 chr7:39989792-39989801 chr7:39989901-39989911 chr7:39989354-39989368 chr7:39989416-39989430 chr7:39989168-39989179 chr7:39989281-39989295 chr7:39989902-39989911
11	TAF1	chr7:39988499-39990252	A549	lung:	n/a	n/a
12	POLR2A	chr7:39987966-39990607	HepG2	liver:	n/a	n/a
13	EBF1	chr7:39989624-39990077	GM12878	blood:	n/a	n/a
14	CREB1	chr7:39988794-39990047	A549	lung:	n/a	n/a
15	POU2F2	chr7:39988595-39990138	GM12878	blood:	n/a	chr7:39989350-39989362
16	JUND	chr7:39988698-39990319	A549	lung:	n/a	n/a
17	CTCF	chr7:39989694-39989760	GM10266	blood:	n/a	n/a
18	POLR2A	chr7:39988569-39990602	MCF-7	breast:	n/a	n/a
19	GATA3	chr7:39988589-39990236	A549	lung:	n/a	n/a
20	POLR2A	chr7:39988619-39990444	PFSK-1	brain:	n/a	n/a
21	CTCF	chr7:39989600-39989750	GM12869	blood:	n/a	n/a
22	ATF2	chr7:39989525-39990022	GM12878	blood:	n/a	n/a
23	HDAC2	chr7:39989562-39989953	HepG2	liver:	n/a	n/a
24	CCNT2	chr7:39988676-39991582	K562	blood:	n/a	chr7:39989792-39989801 chr7:39989902-39989911
25	MYC	chr7:39988955-39989815	HepG2	liver:	n/a	chr7:39989183-39989193 chr7:39989411-39989421
26	TAF1	chr7:39989616-39990414	ECC-1	luminal epithelium:	n/a	n/a
27	POU2F2	chr7:39989575-39989974	GM12878	blood:	n/a	n/a
28	BHLHE40	chr7:39988791-39990038	K562	blood:	n/a	chr7:39989452-39989468 chr7:39989459-39989475 chr7:39989457-39989473
29	JUND	chr7:39988688-39989974	K562	blood:	n/a	n/a
30	YY1	chr7:39989575-39990022	GM12891	blood:	n/a	chr7:39989877-39989891
31	CTCF	chr7:39989680-39989830	HEEpiC	esophagus:	n/a	chr7:39989751-39989764
32	CREB1	chr7:39989550-39990059	H1-hESC	embryonic stem cell:	n/a	n/a
33	SMARCB1	chr7:39988697-39991718	Hela-S3	cervix:	n/a	n/a
34	RFX5	chr7:39989682-39990022	GM12878	blood:	n/a	n/a
35	BCL11A	chr7:39989551-39990003	GM12878	blood:	n/a	chr7:39989938-39989951
36	POLR2A	chr7:39988696-39990690	A549	lung:	n/a	n/a
37	PAX5	chr7:39989563-39989978	GM12891	blood:	n/a	n/a
38	EGR1	chr7:39988791-39990810	K562	blood:	n/a	chr7:39988824-39988848 chr7:39989934-39989944 chr7:39989934-39989945 chr7:39989184-39989194 chr7:39989897-39989910 chr7:39989107-39989116 chr7:39990393-39990407 chr7:39989782-39989795 chr7:39989013-39989027
39	EBF1	chr7:39989571-39990067	GM12878	blood:	n/a	n/a
40	POU2F2	chr7:39989516-39990085	GM12891	blood:	n/a	n/a
41	SIN3AK20	chr7:39988698-39991685	PANC-1	pancreas:	n/a	n/a
42	CTCF	chr7:39989660-39989810	AG04449	skin:	n/a	chr7:39989751-39989764
43	POLR2A	chr7:39988029-39991666	GM18951	blood:	n/a	n/a
44	MAX	chr7:39988507-39990207	MCF-7	breast:	n/a	chr7:39989183-39989193 chr7:39989411-39989421
45	TAF1	chr7:39989582-39990028	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr7:39988560-39990091	PFSK-1	brain:	n/a	n/a
47	PML	chr7:39989540-39990067	K562	blood:	n/a	n/a
48	POLR2A	chr7:39988732-39989919	HepG2	liver:	n/a	n/a
49	E2F4	chr7:39989642-39989968	GM12878	blood:	n/a	chr7:39989896-39989905
50	PAX5	chr7:39989543-39989986	GM12892	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:39989723-39989773	IMR90	lung:	fetal
2	chr7:39989723-39989773	SAEC	small airway:	n/a
3	chr7:39989723-39989773	GM06990	blood:	n/a
4	chr7:39989723-39989773	Hela-S3	cervix:	n/a
5	chr7:39989723-39989773	HIPEpiC	eye:	n/a
6	chr7:39989723-39989773	ProgFib	skin:	n/a
7	chr7:39989723-39989773	SK-N-MC	brain:	n/a
8	chr7:39989723-39989773	HCF	heart:	n/a
9	chr7:39989723-39989773	PFSK-1	brain:	n/a
10	chr7:39989723-39989773	HCM	heart:	n/a
11	chr7:39989723-39989773	BE2_C	brain:	n/a
12	chr7:39989723-39989773	RPTEC	kidney:	n/a
13	chr7:39989723-39989773	GM12892	blood:	n/a
14	chr7:39989723-39989773	A549	lung:	n/a
15	chr7:39989723-39989773	H1-hESC	embryonic stem cell:	embryo
16	chr7:39989723-39989773	HCT-116	colon:	n/a
17	chr7:39989723-39989773	AG04449	skin:	fetal
18	chr7:39989723-39989773	SK-N-SH	brain:	n/a
19	chr7:39989723-39989773	PrEC	prostate:	n/a
20	chr7:39989723-39989773	AG04450	lung:	fetal
21	chr7:39989723-39989773	ovcar-3	ovarian:	n/a
22	chr7:39989723-39989773	SK-N-SH_RA	brain:	n/a
23	chr7:39989723-39989773	HUVEC	blood vessel:	n/a
24	chr7:39989723-39989773	Jurkat	blood:	n/a
25	chr7:39989723-39989773	HEEpiC	esophagus:	n/a
26	chr7:39989723-39989773	PANC-1	pancreas:	n/a
27	chr7:39989723-39989773	LNCaP	prostate:	n/a
28	chr7:39989723-39989773	HRPEpiC	eye:	n/a
29	chr7:39989723-39989773	HCPEpiC	choroid plexus:	n/a
30	chr7:39989723-39989773	SKMC	muscle:	n/a
31	chr7:39989723-39989773	NT2-D1	testis:	n/a
32	chr7:39989723-39989773	Caco-2	colon:	n/a
33	chr7:39989723-39989773	NB4	blood:	n/a
34	chr7:39989723-39989773	NH-A	brain:	n/a
35	chr7:39989723-39989773	HRCEpiC	kidney:	n/a
36	chr7:39989723-39989773	HAEpiC	amniotic membrane:	n/a
37	chr7:39989723-39989773	ECC-1	luminal epithelium:	n/a
38	chr7:39989723-39989773	AG10803	skin:	n/a
39	chr7:39989723-39989773	AoSMC	blood vessel:	n/a
40	chr7:39989723-39989773	NHBE	bronchial:	n/a
41	chr7:39989723-39989773	HPAEpiC	pulmonary alveolar:	n/a
42	chr7:39989723-39989773	MCF-7	breast:	n/a
43	chr7:39989723-39989773	HL-60	blood:	n/a
44	chr7:39989723-39989773	T-47D	breast:	n/a
45	chr7:39989723-39989773	K562	blood:	n/a
46	chr7:39989723-39989773	NHDF-neo	bronchial:	n/a
47	chr7:39989723-39989773	HepG2	liver:	n/a
48	chr7:39989723-39989773	HRE	kidney:	n/a
49	chr7:39989723-39989773	HNPCEpiC	eye:	n/a
50	chr7:39989723-39989773	U87	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:39663090..39665724-chr7:39988469..39990285,2	MCF-7	breast:
2	chr16:85060770..85061475-chr7:39989435..39989944,2	Hela-S3	cervix:
3	chr11:76155227..76155947-chr7:39989290..39990183,2	Hela-S3	cervix:
4	chr7:39989281..39990257-chr9:4679240..4680185,2	Hela-S3	cervix:
5	chr22:39713147..39715672-chr7:39989128..39991236,2	MCF-7	breast:
6	chr1:117909739..117910357-chr7:39988909..39989757,2	Hela-S3	cervix:
7	chr7:39987318..39990027-chr8:101962750..101965742,2	MCF-7	breast:
8	chr7:39989010..39992398-chr7:40024722..40029040,5	MCF-7	breast:
9	chr6:26157666..26158376-chr7:39988958..39989905,3	Hela-S3	cervix:
10	chr7:39989088..39989799-chr9:5437668..5438233,2	Hela-S3	cervix:
11	chr10:75011864..75012841-chr7:39989467..39990350,2	NB4	blood:
12	chr7:39987721..39990242-chr7:40174056..40176267,2	MCF-7	breast:
13	chr5:180236713..180237305-chr7:39989209..39989914,2	Hela-S3	cervix:
14	chr14:96968408..96969093-chr7:39989276..39989838,2	Hela-S3	cervix:
15	chr14:92587219..92588097-chr7:39989268..39989812,2	Hela-S3	cervix:
16	chr20:48598768..48599760-chr7:39989242..39989944,2	Hela-S3	cervix:
17	chr7:39985235..39991458-chr7:40172332..40176244,8	K562	blood:

Variant related genes	Relation type
ENSG00000259826	TF binding region
CDK13	TF binding region
CDK13	CpG island
ENSG00000259826	CpG island
ENSG00000182180	Chromatin interaction
ENSG00000175600	Chromatin interaction
ENSG00000106993	Chromatin interaction
ENSG00000255135	Chromatin interaction
ENSG00000065883	Chromatin interaction
ENSG00000183648	Chromatin interaction
ENSG00000124216	Chromatin interaction
ENSG00000090060	Chromatin interaction
ENSG00000198162	Chromatin interaction
ENSG00000100316	Chromatin interaction
ENSG00000273061	Chromatin interaction
ENSG00000131446	Chromatin interaction
ENSG00000164924	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000227540	Chromatin interaction
ENSG00000260806	Chromatin interaction
ENSG00000263764	Chromatin interaction
ENSG00000168303	Chromatin interaction
ENSG00000006451	Chromatin interaction
ENSG00000107020	Chromatin interaction
ENSG00000135709	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887973	chr7:39772654-40110720	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	nsv887975	chr7:39858378-40124137	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
3	nsv887976	chr7:39874986-40018693	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv887977	chr7:39885541-40018693	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	esv3335126	chr7:39989577-39991875	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	33 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	chr7:39987800-39992800	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr7:39987800-39993200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr7:39987800-39993400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:39988000-39990600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr7:39988000-39991400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:39988000-39991400	Active TSS	Esophagus	oesophagus
7	chr7:39988000-39991800	Active TSS	Gastric	stomach
8	chr7:39988000-39991800	Active TSS	Left Ventricle	heart
9	chr7:39988000-39991800	Active TSS	Pancreas	Pancrea
10	chr7:39988000-39992000	Active TSS	Stomach Mucosa	stomach
11	chr7:39988000-39992200	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr7:39988000-39992400	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr7:39988000-39992800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:39988000-39993000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr7:39988000-39993200	Active TSS	HSMM	muscle
16	chr7:39988000-39993400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:39988000-39993400	Active TSS	Osteobl	bone
18	chr7:39988000-39993600	Active TSS	Colonic Mucosa	Colon
19	chr7:39988000-39993800	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr7:39988000-39993800	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr7:39988000-39994000	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr7:39988200-39991000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:39988200-39991800	Active TSS	Lung	lung
24	chr7:39988200-39992200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr7:39988200-39992800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr7:39988200-39993200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr7:39988200-39993200	Active TSS	H9 Cell Line	embryonic stem cell
28	chr7:39988200-39993200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr7:39988200-39993200	Active TSS	Muscle Satellite Cultured Cells	--
30	chr7:39988200-39993200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr7:39988200-39993200	Active TSS	Colon Smooth Muscle	Colon
32	chr7:39988200-39993200	Active TSS	Sigmoid Colon	Sigmoid Colon
33	chr7:39988200-39993200	Active TSS	A549	lung
34	chr7:39988200-39993200	Active TSS	K562	blood
35	chr7:39988200-39993200	Active TSS	NH-A	brain
36	chr7:39988200-39993200	Active TSS	NHDF-Ad	bronchial
37	chr7:39988200-39993400	Active TSS	Aorta	Aorta
38	chr7:39988200-39993400	Active TSS	Psoas Muscle	Psoas
39	chr7:39988200-39993400	Active TSS	Right Ventricle	heart
40	chr7:39988200-39993600	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr7:39988200-39993800	Active TSS	H1 Cell Line	embryonic stem cell
42	chr7:39988200-39996200	Active TSS	GM12878-XiMat	blood
43	chr7:39988400-39989800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr7:39988400-39989800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr7:39988400-39989800	Active TSS	Brain Germinal Matrix	brain
46	chr7:39988400-39989800	Active TSS	Stomach Smooth Muscle	stomach
47	chr7:39988400-39990200	Active TSS	Fetal Brain Male	brain
48	chr7:39988400-39991000	Active TSS	Dnd41	blood
49	chr7:39988400-39991200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr7:39988400-39991400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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