Variant report

Variant	rs17496102
Chromosome Location	chr7:39989380-39989381
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	RELA	chr7:39988693-39990191	GM19099	blood:	n/a	n/a
2	POLR2A	chr7:39988693-39989536	H1-hESC	embryonic stem cell:	n/a	n/a
3	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
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	MYC	chr7:39988576-39990092	K562	blood:	n/a	chr7:39989183-39989193 chr7:39989411-39989421
8	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
9	CEBPD	chr7:39989002-39989429	HepG2	liver:	n/a	n/a
10	TAF1	chr7:39988499-39990252	A549	lung:	n/a	n/a
11	POLR2A	chr7:39987966-39990607	HepG2	liver:	n/a	n/a
12	CREB1	chr7:39988794-39990047	A549	lung:	n/a	n/a
13	MYC	chr7:39989311-39989461	GM12878	blood:	n/a	chr7:39989411-39989421
14	POU2F2	chr7:39988595-39990138	GM12878	blood:	n/a	chr7:39989350-39989362
15	JUND	chr7:39988698-39990319	A549	lung:	n/a	n/a
16	POLR2A	chr7:39988569-39990602	MCF-7	breast:	n/a	n/a
17	GATA3	chr7:39988589-39990236	A549	lung:	n/a	n/a
18	POLR2A	chr7:39988619-39990444	PFSK-1	brain:	n/a	n/a
19	CCNT2	chr7:39988676-39991582	K562	blood:	n/a	chr7:39989792-39989801 chr7:39989902-39989911
20	MYC	chr7:39988955-39989815	HepG2	liver:	n/a	chr7:39989183-39989193 chr7:39989411-39989421
21	E2F6	chr7:39989048-39989441	K562	blood:	n/a	chr7:39989418-39989427
22	BHLHE40	chr7:39988791-39990038	K562	blood:	n/a	chr7:39989452-39989468 chr7:39989459-39989475 chr7:39989457-39989473
23	YY1	chr7:39988828-39989440	ECC-1	luminal epithelium:	n/a	chr7:39989418-39989429 chr7:39989377-39989391
24	JUND	chr7:39988688-39989974	K562	blood:	n/a	n/a
25	SMARCB1	chr7:39988697-39991718	Hela-S3	cervix:	n/a	n/a
26	TAF1	chr7:39988692-39989483	SK-N-SH	brain:	n/a	n/a
27	YY1	chr7:39989272-39989552	GM12878	blood:	n/a	chr7:39989466-39989475 chr7:39989458-39989469 chr7:39989524-39989535 chr7:39989457-39989471 chr7:39989418-39989429 chr7:39989464-39989475 chr7:39989463-39989472 chr7:39989461-39989472 chr7:39989457-39989466 chr7:39989377-39989391 chr7:39989460-39989474 chr7:39989454-39989468 chr7:39989460-39989469
28	CTCF	chr7:39989266-39989445	MCF-7	breast:	n/a	chr7:39989401-39989414
29	POLR2A	chr7:39988696-39990690	A549	lung:	n/a	n/a
30	STAT3	chr7:39989096-39989399	MCF10A-Er-Src	breast:	n/a	chr7:39989360-39989372
31	STAT3	chr7:39988998-39989413	MCF10A-Er-Src	breast:	n/a	chr7:39989360-39989372
32	ATF2	chr7:39988795-39989521	H1-hESC	embryonic stem cell:	n/a	n/a
33	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
34	RAD21	chr7:39988619-39989442	IMR90	lung:	n/a	chr7:39989395-39989408 chr7:39989012-39989025 chr7:39989124-39989137
35	EGR1	chr7:39988744-39989509	GM12878	blood:	n/a	chr7:39988824-39988848 chr7:39989184-39989194 chr7:39989107-39989116 chr7:39989013-39989027
36	RELA	chr7:39988708-39989415	GM18526	blood:	n/a	n/a
37	SIN3AK20	chr7:39988698-39991685	PANC-1	pancreas:	n/a	n/a
38	POLR2A	chr7:39988029-39991666	GM18951	blood:	n/a	n/a
39	MAX	chr7:39988507-39990207	MCF-7	breast:	n/a	chr7:39989183-39989193 chr7:39989411-39989421
40	POLR2A	chr7:39988560-39990091	PFSK-1	brain:	n/a	n/a
41	POLR2A	chr7:39988732-39989919	HepG2	liver:	n/a	n/a
42	MYC	chr7:39988858-39989576	MCF-7	breast:	n/a	chr7:39989183-39989193 chr7:39989411-39989421
43	REST	chr7:39988682-39989448	PFSK-1	brain:	n/a	chr7:39989330-39989343
44	MYC	chr7:39988677-39990041	A549	lung:	n/a	chr7:39989183-39989193 chr7:39989411-39989421
45	ZNF143	chr7:39988790-39990121	Hela-S3	cervix:	n/a	chr7:39989377-39989387 chr7:39990011-39990021
46	ZNF143	chr7:39988813-39989798	H1-hESC	embryonic stem cell:	n/a	chr7:39989377-39989387
47	REST	chr7:39988663-39989500	SK-N-SH	brain:	n/a	chr7:39989330-39989343
48	GABPA	chr7:39988551-39990399	K562	blood:	n/a	n/a
49	ELK1	chr7:39988736-39990103	Hela-S3	cervix:	n/a	chr7:39989107-39989116 chr7:39989107-39989116
50	RUNX3	chr7:39988015-39989512	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:39987485..39989678-chr7:40173138..40176244,4	K562	blood:
2	chr7:39663090..39665724-chr7:39988469..39990285,2	MCF-7	breast:
3	chr19:48824897..48825730-chr7:39988705..39989640,2	NB4	blood:
4	chr1:41156987..41157841-chr7:39988968..39989713,2	NB4	blood:
5	chr19:39897400..39897939-chr7:39988698..39989697,2	Hela-S3	cervix:
6	chr7:39605012..39607338-chr7:39986740..39989686,2	K562	blood:
7	chr11:76155227..76155947-chr7:39989290..39990183,2	Hela-S3	cervix:
8	chr19:1268912..1269455-chr7:39988552..39989529,2	Hela-S3	cervix:
9	chr7:39989281..39990257-chr9:4679240..4680185,2	Hela-S3	cervix:
10	chr22:39713147..39715672-chr7:39989128..39991236,2	MCF-7	breast:
11	chr1:117909739..117910357-chr7:39988909..39989757,2	Hela-S3	cervix:
12	chr7:39987318..39990027-chr8:101962750..101965742,2	MCF-7	breast:
13	chr7:39989010..39992398-chr7:40024722..40029040,5	MCF-7	breast:
14	chr11:96122465..96123203-chr7:39988642..39989631,2	Hela-S3	cervix:
15	chr6:26157666..26158376-chr7:39988958..39989905,3	Hela-S3	cervix:
16	chr7:39989088..39989799-chr9:5437668..5438233,2	Hela-S3	cervix:
17	chr13:115079770..115080277-chr7:39988952..39989607,2	HCT-116	colon:
18	chr7:39987721..39990242-chr7:40174056..40176267,2	MCF-7	breast:
19	chr5:180236713..180237305-chr7:39989209..39989914,2	Hela-S3	cervix:
20	chr14:96968408..96969093-chr7:39989276..39989838,2	Hela-S3	cervix:
21	chr6:74230266..74231191-chr7:39988525..39989555,3	Hela-S3	cervix:
22	chr12:56551913..56552508-chr7:39988805..39989416,2	Hela-S3	cervix:
23	chr14:92587219..92588097-chr7:39989268..39989812,2	Hela-S3	cervix:
24	chr20:48598768..48599760-chr7:39989242..39989944,2	Hela-S3	cervix:
25	chr7:39985235..39991458-chr7:40172332..40176244,8	K562	blood:

Variant related genes	Relation type
CDK13	TF binding region
ENSG00000259826	TF binding region
ENSG00000227172	Chromatin interaction
ENSG00000198824	Chromatin interaction
ENSG00000105479	Chromatin interaction
ENSG00000090060	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000006451	Chromatin interaction
ENSG00000183648	Chromatin interaction
ENSG00000198162	Chromatin interaction
ENSG00000164924	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000175600	Chromatin interaction
ENSG00000131446	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000149231	Chromatin interaction
ENSG00000168303	Chromatin interaction
ENSG00000260806	Chromatin interaction
ENSG00000107020	Chromatin interaction
ENSG00000100316	Chromatin interaction
ENSG00000183340	Chromatin interaction
ENSG00000106993	Chromatin interaction
ENSG00000124216	Chromatin interaction
ENSG00000273061	Chromatin interaction
ENSG00000099622	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000272145	Chromatin interaction
ENSG00000065883	Chromatin interaction
ENSG00000066136	Chromatin interaction
ENSG00000263764	Chromatin interaction
ENSG00000241127	Chromatin interaction
ENSG00000128016	Chromatin interaction
ENSG00000255135	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1146042	0.86[ASN][1000 genomes]
rs1798988	0.84[ASN][1000 genomes]
rs699513	0.89[ASN][1000 genomes]
rs773407	0.95[ASN][1000 genomes]
rs798852	0.89[ASN][1000 genomes]
rs798854	0.89[ASN][1000 genomes]
rs798857	0.83[ASN][1000 genomes]
rs798863	0.82[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	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

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	chr7:39988000-39989600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:39988000-39990600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:39988000-39991400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:39988000-39991400	Active TSS	Esophagus	oesophagus
8	chr7:39988000-39991800	Active TSS	Gastric	stomach
9	chr7:39988000-39991800	Active TSS	Left Ventricle	heart
10	chr7:39988000-39991800	Active TSS	Pancreas	Pancrea
11	chr7:39988000-39992000	Active TSS	Stomach Mucosa	stomach
12	chr7:39988000-39992200	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr7:39988000-39992400	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr7:39988000-39992800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:39988000-39993000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr7:39988000-39993200	Active TSS	HSMM	muscle
17	chr7:39988000-39993400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr7:39988000-39993400	Active TSS	Osteobl	bone
19	chr7:39988000-39993600	Active TSS	Colonic Mucosa	Colon
20	chr7:39988000-39993800	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr7:39988000-39993800	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr7:39988000-39994000	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr7:39988200-39989600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr7:39988200-39991000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr7:39988200-39991800	Active TSS	Lung	lung
26	chr7:39988200-39992200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr7:39988200-39992800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr7:39988200-39993200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr7:39988200-39993200	Active TSS	H9 Cell Line	embryonic stem cell
30	chr7:39988200-39993200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr7:39988200-39993200	Active TSS	Muscle Satellite Cultured Cells	--
32	chr7:39988200-39993200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:39988200-39993200	Active TSS	Colon Smooth Muscle	Colon
34	chr7:39988200-39993200	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr7:39988200-39993200	Active TSS	A549	lung
36	chr7:39988200-39993200	Active TSS	K562	blood
37	chr7:39988200-39993200	Active TSS	NH-A	brain
38	chr7:39988200-39993200	Active TSS	NHDF-Ad	bronchial
39	chr7:39988200-39993400	Active TSS	Aorta	Aorta
40	chr7:39988200-39993400	Active TSS	Psoas Muscle	Psoas
41	chr7:39988200-39993400	Active TSS	Right Ventricle	heart
42	chr7:39988200-39993600	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr7:39988200-39993800	Active TSS	H1 Cell Line	embryonic stem cell
44	chr7:39988200-39996200	Active TSS	GM12878-XiMat	blood
45	chr7:39988400-39989600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr7:39988400-39989800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr7:39988400-39989800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr7:39988400-39989800	Active TSS	Brain Germinal Matrix	brain
49	chr7:39988400-39989800	Active TSS	Stomach Smooth Muscle	stomach
50	chr7:39988400-39990200	Active TSS	Fetal Brain Male	brain

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