Variant report

Variant	rs17236639
Chromosome Location	chr5:68710745-68710746
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	CTCF	chr5:68710704-68710914	GM12878	blood:	n/a	chr5:68710817-68710830 chr5:68710814-68710827
2	CHD1	chr5:68710706-68710769	GM12878	blood:	n/a	n/a
3	ELF1	chr5:68710688-68711203	HepG2	liver:	n/a	chr5:68710913-68710925
4	CTCF	chr5:68710741-68710906	Spleen_OC	spleen:	n/a	chr5:68710817-68710830 chr5:68710814-68710827
5	TCF7L2	chr5:68710697-68711605	HCT-116	colon:	n/a	n/a
6	EBF1	chr5:68710662-68710931	GM12878	blood:	n/a	n/a
7	EP300	chr5:68710616-68711280	H1-hESC	embryonic stem cell:	n/a	n/a
8	SIN3AK20	chr5:68710620-68711496	PANC-1	pancreas:	n/a	n/a
9	CTCF	chr5:68710434-68711266	A549	lung:	n/a	chr5:68710817-68710830 chr5:68710814-68710827
10	CTCF	chr5:68710720-68710870	HPF	lung:	n/a	chr5:68710817-68710830 chr5:68710814-68710827
11	BHLHE40	chr5:68710670-68711219	HepG2	liver:	n/a	n/a
12	REST	chr5:68710725-68711112	HepG2	liver:	n/a	n/a
13	RCOR1	chr5:68710632-68711267	Hela-S3	cervix:	n/a	n/a
14	MYBL2	chr5:68710607-68711131	HepG2	liver:	n/a	n/a
15	GATA1	chr5:68710558-68711262	PBDE	blood:	n/a	chr5:68710731-68710739 chr5:68710695-68710708
16	POLR2A	chr5:68710658-68711765	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr5:68710732-68711780	MCF-7	breast:	n/a	n/a
18	MYC	chr5:68710626-68711467	A549	lung:	n/a	chr5:68710921-68710931 chr5:68711018-68711027 chr5:68711017-68711028 chr5:68711016-68711029 chr5:68711018-68711027
19	SMC3	chr5:68710657-68711015	GM12878	blood:	n/a	chr5:68710821-68710828
20	CTCF	chr5:68710735-68710919	GM10266	blood:	n/a	chr5:68710817-68710830 chr5:68710814-68710827
21	RUNX3	chr5:68710626-68711344	GM12878	blood:	n/a	n/a
22	CTCF	chr5:68710720-68710870	GM06990	blood:	n/a	chr5:68710817-68710830 chr5:68710814-68710827
23	MYC	chr5:68710682-68711207	H1-hESC	embryonic stem cell:	n/a	chr5:68710921-68710931 chr5:68711018-68711027 chr5:68711017-68711028 chr5:68711016-68711029 chr5:68711018-68711027
24	SIN3AK20	chr5:68710563-68711936	MCF-7	breast:	n/a	n/a
25	TCF3	chr5:68710740-68711303	GM12878	blood:	n/a	n/a
26	PML	chr5:68710448-68711632	GM12878	blood:	n/a	n/a
27	USF1	chr5:68710724-68711324	H1-hESC	embryonic stem cell:	n/a	n/a
28	RAD21	chr5:68710654-68710975	IMR90	lung:	n/a	chr5:68710814-68710828
29	CTCF	chr5:68710551-68711124	MCF-7	breast:	n/a	chr5:68710817-68710830 chr5:68710814-68710827
30	MTA3	chr5:68710569-68711607	GM12878	blood:	n/a	n/a
31	RAD21	chr5:68710683-68711067	GM12878	blood:	n/a	chr5:68710814-68710828
32	POLR2A	chr5:68710637-68711694	HepG2	liver:	n/a	n/a
33	POLR2A	chr5:68710644-68711700	HCT-116	colon:	n/a	n/a
34	YY1	chr5:68710734-68711070	GM12878	blood:	n/a	chr5:68710918-68710932 chr5:68710920-68710929 chr5:68710986-68710997
35	RAD21	chr5:68710664-68711309	HepG2	liver:	n/a	chr5:68710814-68710828
36	POLR2A	chr5:68710666-68711761	MCF-7	breast:	n/a	n/a
37	CTCF	chr5:68710740-68710890	BJ	skin:	n/a	chr5:68710817-68710830 chr5:68710814-68710827
38	MAZ	chr5:68710665-68711412	Hela-S3	cervix:	n/a	chr5:68710921-68710931 chr5:68711018-68711027 chr5:68711017-68711028 chr5:68711016-68711029 chr5:68711018-68711027
39	RAD21	chr5:68710584-68711288	A549	lung:	n/a	chr5:68710814-68710828
40	POLR2A	chr5:68710728-68711759	Hela-S3	cervix:	n/a	n/a
41	RAD21	chr5:68710580-68711293	ECC-1	luminal epithelium:	n/a	chr5:68710814-68710828
42	POLR2A	chr5:68710613-68711809	H1-hESC	embryonic stem cell:	n/a	n/a
43	HEY1	chr5:68710695-68711333	HepG2	liver:	n/a	chr5:68710983-68710998
44	POLR2A	chr5:68710552-68711858	GM12878	blood:	n/a	n/a
45	HDAC2	chr5:68710693-68711160	HepG2	liver:	n/a	n/a
46	CTCF	chr5:68710740-68710890	GM12878	blood:	n/a	chr5:68710817-68710830 chr5:68710814-68710827
47	WRNIP1	chr5:68710645-68710777	GM12878	blood:	n/a	n/a
48	POLR2A	chr5:68710716-68711447	GM12878	blood:	n/a	n/a
49	ELF1	chr5:68710595-68711483	MCF-7	breast:	n/a	chr5:68710913-68710925
50	NFATC1	chr5:68710730-68711234	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:68664291..68666075-chr5:68709843..68712396,3	MCF-7	breast:
2	chr5:68709515..68715463-chr5:68785927..68791978,14	MCF-7	breast:
3	chr5:68708231..68714128-chr5:68786986..68792913,14	MCF-7	breast:
4	chr5:68664280..68666817-chr5:68709824..68711367,2	MCF-7	breast:

Variant related genes	Relation type
MARVELD2	TF binding region
ENSG00000085231	Chromatin interaction
ENSG00000152942	Chromatin interaction
ENSG00000197822	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs17236219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17236380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17236422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17236450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17236618	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4252222	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4252226	1.00[EUR][1000 genomes]
rs4252229	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55754329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55764482	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56112110	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56362385	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57344277	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57714822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58172827	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59233462	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59799008	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60644166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61290150	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6861518	1.00[EUR][1000 genomes]
rs6876889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73772384	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73772537	1.00[AMR][1000 genomes]
rs73772541	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73772542	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73772544	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73772545	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73772550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881767	chr5:68625786-68733698	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1018410	chr5:68692244-68822384	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68666600-68710800	Weak transcription	Esophagus	oesophagus
2	chr5:68666800-68710800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:68666800-68710800	Weak transcription	Psoas Muscle	Psoas
4	chr5:68667200-68710800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr5:68668000-68713000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:68668800-68712400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:68690200-68710800	Weak transcription	Gastric	stomach
8	chr5:68690800-68711200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr5:68691600-68710800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:68696800-68710800	Weak transcription	Aorta	Aorta
11	chr5:68696800-68711000	Weak transcription	Small Intestine	intestine
12	chr5:68697000-68710800	Weak transcription	Pancreas	Pancrea
13	chr5:68697800-68717000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr5:68701200-68713800	Weak transcription	K562	blood
15	chr5:68704600-68711200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:68705200-68710800	Weak transcription	Brain Angular Gyrus	brain
17	chr5:68705400-68710800	Weak transcription	Lung	lung
18	chr5:68707800-68710800	Weak transcription	Colon Smooth Muscle	Colon
19	chr5:68707800-68710800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr5:68707800-68711000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:68707800-68712800	Weak transcription	HSMMtube	muscle
22	chr5:68708200-68711000	Strong transcription	HSMM	muscle
23	chr5:68709200-68710800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr5:68709800-68711200	Active TSS	Primary B cells from cord blood	blood
25	chr5:68709800-68711800	Strong transcription	Dnd41	blood
26	chr5:68710000-68712000	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr5:68710200-68710800	Weak transcription	Left Ventricle	heart
28	chr5:68710200-68710800	Weak transcription	Ovary	ovary
29	chr5:68710200-68712200	Active TSS	Fetal Kidney	kidney
30	chr5:68710400-68710800	Weak transcription	Adipose Nuclei	Adipose
31	chr5:68710400-68710800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr5:68710400-68710800	Enhancers	Brain Substantia Nigra	brain
33	chr5:68710400-68710800	Enhancers	Fetal Heart	heart
34	chr5:68710400-68710800	Weak transcription	Fetal Muscle Leg	muscle
35	chr5:68710400-68710800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr5:68710400-68711200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr5:68710400-68711200	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr5:68710400-68711400	Active TSS	GM12878-XiMat	blood
39	chr5:68710400-68711600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:68710400-68712000	Active TSS	A549	lung
41	chr5:68710400-68712200	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr5:68710400-68712200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr5:68710400-68712600	Active TSS	H1 Cell Line	embryonic stem cell
44	chr5:68710600-68710800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr5:68710600-68710800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr5:68710600-68710800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr5:68710600-68710800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:68710600-68710800	Enhancers	Primary B cells from peripheral blood	blood
49	chr5:68710600-68710800	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
50	chr5:68710600-68710800	Active TSS	Primary hematopoietic stem cells	blood

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