Variant report

Variant	rs17537614
Chromosome Location	chr7:39988801-39988802
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	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	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
6	CHD1	chr7:39988648-39989013	H1-hESC	embryonic stem cell:	n/a	n/a
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	TAF1	chr7:39988499-39990252	A549	lung:	n/a	n/a
10	POLR2A	chr7:39987966-39990607	HepG2	liver:	n/a	n/a
11	CREB1	chr7:39988794-39990047	A549	lung:	n/a	n/a
12	PBX3	chr7:39988659-39989342	A549	lung:	n/a	n/a
13	POU2F2	chr7:39988595-39990138	GM12878	blood:	n/a	chr7:39989350-39989362
14	JUND	chr7:39988698-39990319	A549	lung:	n/a	n/a
15	WRNIP1	chr7:39988550-39989348	GM12878	blood:	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	BHLHE40	chr7:39988791-39990038	K562	blood:	n/a	chr7:39989452-39989468 chr7:39989459-39989475 chr7:39989457-39989473
21	SIN3AK20	chr7:39988731-39989075	PANC-1	pancreas:	n/a	n/a
22	EGR1	chr7:39988746-39989134	GM12878	blood:	n/a	chr7:39988824-39988848 chr7:39989107-39989116 chr7:39989013-39989027
23	JUND	chr7:39988688-39989974	K562	blood:	n/a	n/a
24	TAF7	chr7:39988695-39989270	H1-hESC	embryonic stem cell:	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	POLR2A	chr7:39988696-39990690	A549	lung:	n/a	n/a
28	ATF2	chr7:39988795-39989521	H1-hESC	embryonic stem cell:	n/a	n/a
29	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
30	RAD21	chr7:39988619-39989442	IMR90	lung:	n/a	chr7:39989395-39989408 chr7:39989012-39989025 chr7:39989124-39989137
31	EGR1	chr7:39988744-39989509	GM12878	blood:	n/a	chr7:39988824-39988848 chr7:39989184-39989194 chr7:39989107-39989116 chr7:39989013-39989027
32	RELA	chr7:39988708-39989415	GM18526	blood:	n/a	n/a
33	SIN3AK20	chr7:39988698-39991685	PANC-1	pancreas:	n/a	n/a
34	POLR2A	chr7:39988029-39991666	GM18951	blood:	n/a	n/a
35	MAX	chr7:39988507-39990207	MCF-7	breast:	n/a	chr7:39989183-39989193 chr7:39989411-39989421
36	NFATC1	chr7:39988671-39989267	GM12878	blood:	n/a	n/a
37	POLR2A	chr7:39988560-39990091	PFSK-1	brain:	n/a	n/a
38	POLR2A	chr7:39988732-39989919	HepG2	liver:	n/a	n/a
39	REST	chr7:39988682-39989448	PFSK-1	brain:	n/a	chr7:39989330-39989343
40	MYC	chr7:39988677-39990041	A549	lung:	n/a	chr7:39989183-39989193 chr7:39989411-39989421
41	ZNF143	chr7:39988790-39990121	Hela-S3	cervix:	n/a	chr7:39989377-39989387 chr7:39990011-39990021
42	ATF3	chr7:39988701-39989220	A549	lung:	n/a	n/a
43	REST	chr7:39988663-39989500	SK-N-SH	brain:	n/a	chr7:39989330-39989343
44	GABPA	chr7:39988551-39990399	K562	blood:	n/a	n/a
45	SIN3AK20	chr7:39988676-39989376	A549	lung:	n/a	n/a
46	ELK1	chr7:39988736-39990103	Hela-S3	cervix:	n/a	chr7:39989107-39989116 chr7:39989107-39989116
47	RUNX3	chr7:39988015-39989512	GM12878	blood:	n/a	n/a
48	POLR2A	chr7:39987755-39991690	Hela-S3	cervix:	n/a	n/a
49	BATF	chr7:39988644-39989114	GM12878	blood:	n/a	n/a
50	ELF1	chr7:39988503-39990372	SK-N-SH	brain:	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

No.	Distal block	Cell Line	Cell type
1	chr1:94311521..94312144-chr7:39988387..39989256,2	HCT-116	colon:
2	chr7:39987485..39989678-chr7:40173138..40176244,4	K562	blood:
3	chr7:39663090..39665724-chr7:39988469..39990285,2	MCF-7	breast:
4	chr19:48824897..48825730-chr7:39988705..39989640,2	NB4	blood:
5	chr7:39987353..39988943-chr7:40114287..40116137,2	K562	blood:
6	chr19:39897400..39897939-chr7:39988698..39989697,2	Hela-S3	cervix:
7	chr2:63815667..63816442-chr7:39988724..39989292,2	NB4	blood:
8	chr7:39605012..39607338-chr7:39986740..39989686,2	K562	blood:
9	chr19:1268912..1269455-chr7:39988552..39989529,2	Hela-S3	cervix:
10	chr17:33914316..33914947-chr7:39988751..39989359,2	NB4	blood:
11	chr7:39988519..39989328-chr8:144911030..144911895,2	HCT-116	colon:
12	chr1:150550230..150550897-chr7:39988646..39989310,2	Hela-S3	cervix:
13	chr7:39987649..39989294-chr7:40160123..40163099,2	K562	blood:
14	chr7:39987318..39990027-chr8:101962750..101965742,2	MCF-7	breast:
15	chr11:96122465..96123203-chr7:39988642..39989631,2	Hela-S3	cervix:
16	chr19:1239438..1240363-chr7:39988573..39989148,2	HCT-116	colon:
17	chr11:107879571..107880146-chr7:39988538..39989329,2	Hela-S3	cervix:
18	chr7:39963368..39965638-chr7:39986641..39989237,2	K562	blood:
19	chr7:39986663..39989008-chr7:40035472..40037902,2	K562	blood:
20	chr7:39987721..39990242-chr7:40174056..40176267,2	MCF-7	breast:
21	chr6:74230266..74231191-chr7:39988525..39989555,3	Hela-S3	cervix:
22	chr7:39985235..39991458-chr7:40172332..40176244,8	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C7orf11-1	chr7:39987121-39989354	ENSG00000259826.1

Variant related genes	Relation type
CDK13	TF binding region
ENSG00000006125	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000099622	Chromatin interaction
ENSG00000006451	Chromatin interaction
ENSG00000166266	Chromatin interaction
ENSG00000241127	Chromatin interaction
ENSG00000128016	Chromatin interaction
ENSG00000168303	Chromatin interaction
ENSG00000105479	Chromatin interaction
ENSG00000149231	Chromatin interaction
ENSG00000179950	Chromatin interaction
ENSG00000014641	Chromatin interaction
ENSG00000183340	Chromatin interaction
ENSG00000175600	Chromatin interaction
ENSG00000143951	Chromatin interaction
ENSG00000164924	Chromatin interaction
ENSG00000227172	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11973952	0.83[AMR][1000 genomes]
rs17496116	0.83[AMR][1000 genomes]
rs17496579	0.83[AMR][1000 genomes]
rs17496598	0.83[AMR][1000 genomes]
rs17496641	0.83[AMR][1000 genomes]
rs17537760	0.83[AMR][1000 genomes]
rs17538209	0.83[AMR][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	chr7:39987600-39989000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr7:39987800-39992800	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr7:39987800-39993200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr7:39987800-39993400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr7:39988000-39989000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr7:39988000-39989000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
7	chr7:39988000-39989600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:39988000-39990600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr7:39988000-39991400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:39988000-39991400	Active TSS	Esophagus	oesophagus
11	chr7:39988000-39991800	Active TSS	Gastric	stomach
12	chr7:39988000-39991800	Active TSS	Left Ventricle	heart
13	chr7:39988000-39991800	Active TSS	Pancreas	Pancrea
14	chr7:39988000-39992000	Active TSS	Stomach Mucosa	stomach
15	chr7:39988000-39992200	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr7:39988000-39992400	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr7:39988000-39992800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr7:39988000-39993000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr7:39988000-39993200	Active TSS	HSMM	muscle
20	chr7:39988000-39993400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr7:39988000-39993400	Active TSS	Osteobl	bone
22	chr7:39988000-39993600	Active TSS	Colonic Mucosa	Colon
23	chr7:39988000-39993800	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr7:39988000-39993800	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr7:39988000-39994000	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr7:39988200-39989600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr7:39988200-39991000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr7:39988200-39991800	Active TSS	Lung	lung
29	chr7:39988200-39992200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr7:39988200-39992800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr7:39988200-39993200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr7:39988200-39993200	Active TSS	H9 Cell Line	embryonic stem cell
33	chr7:39988200-39993200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr7:39988200-39993200	Active TSS	Muscle Satellite Cultured Cells	--
35	chr7:39988200-39993200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr7:39988200-39993200	Active TSS	Colon Smooth Muscle	Colon
37	chr7:39988200-39993200	Active TSS	Sigmoid Colon	Sigmoid Colon
38	chr7:39988200-39993200	Active TSS	A549	lung
39	chr7:39988200-39993200	Active TSS	K562	blood
40	chr7:39988200-39993200	Active TSS	NH-A	brain
41	chr7:39988200-39993200	Active TSS	NHDF-Ad	bronchial
42	chr7:39988200-39993400	Active TSS	Aorta	Aorta
43	chr7:39988200-39993400	Active TSS	Psoas Muscle	Psoas
44	chr7:39988200-39993400	Active TSS	Right Ventricle	heart
45	chr7:39988200-39993600	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr7:39988200-39993800	Active TSS	H1 Cell Line	embryonic stem cell
47	chr7:39988200-39996200	Active TSS	GM12878-XiMat	blood
48	chr7:39988400-39989000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr7:39988400-39989000	Active TSS	Fetal Heart	heart
50	chr7:39988400-39989600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links