Variant report

Variant	rs5744538
Chromosome Location	chr5:74806888-74806889
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	EP300	chr5:74806228-74807730	ECC-1	luminal epithelium:	n/a	chr5:74807358-74807372 chr5:74807368-74807382
2	E2F6	chr5:74806600-74807029	A549	lung:	n/a	chr5:74806845-74806856 chr5:74806842-74806851
3	YY1	chr5:74806558-74808112	K562	blood:	n/a	chr5:74807423-74807442 chr5:74806850-74806861 chr5:74807425-74807435 chr5:74807425-74807447 chr5:74806737-74806748 chr5:74807422-74807442 chr5:74807426-74807434
4	ZNF263	chr5:74805797-74808068	HEK293-T-REx	kidney:	n/a	chr5:74807566-74807575 chr5:74807116-74807137 chr5:74807154-74807175
5	YY1	chr5:74806864-74808023	A549	lung:	n/a	chr5:74807423-74807442 chr5:74807425-74807435 chr5:74807425-74807447 chr5:74807422-74807442 chr5:74807426-74807434
6	CREB1	chr5:74806657-74808264	GM12878	blood:	n/a	n/a
7	RCOR1	chr5:74806336-74807047	K562	blood:	n/a	n/a
8	POLR2A	chr5:74806774-74807027	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr5:74806410-74808835	GM18505	blood:	n/a	n/a
10	TAF1	chr5:74806545-74808069	H1-neurons	neurons:	n/a	n/a
11	MAX	chr5:74805816-74808456	NB4	blood:	n/a	n/a
12	MAX	chr5:74806696-74806953	K562	blood:	n/a	n/a
13	BHLHE40	chr5:74806658-74808093	HepG2	liver:	n/a	n/a
14	MAX	chr5:74806484-74808141	HepG2	liver:	n/a	n/a
15	POLR2A	chr5:74806479-74808595	PBDE	blood:	n/a	n/a
16	SMARCC2	chr5:74806421-74808079	Hela-S3	cervix:	n/a	chr5:74807711-74807720
17	HA-E2F1	chr5:74806466-74808228	MCF-7	breast:	n/a	chr5:74806842-74806851
18	SIN3AK20	chr5:74806602-74807928	MCF-7	breast:	n/a	n/a
19	JUND	chr5:74806587-74806953	H1-hESC	embryonic stem cell:	n/a	n/a
20	ELF1	chr5:74806567-74808222	MCF-7	breast:	n/a	chr5:74807967-74807976
21	YY1	chr5:74806780-74808072	HepG2	liver:	n/a	chr5:74807423-74807442 chr5:74806850-74806861 chr5:74807425-74807435 chr5:74807425-74807447 chr5:74807422-74807442 chr5:74807426-74807434
22	E2F6	chr5:74806607-74808295	A549	lung:	n/a	chr5:74806845-74806856 chr5:74806842-74806851
23	YY1	chr5:74806398-74808048	GM12892	blood:	n/a	chr5:74807423-74807442 chr5:74806850-74806861 chr5:74807425-74807435 chr5:74807425-74807447 chr5:74806737-74806748 chr5:74807422-74807442 chr5:74807426-74807434
24	YY1	chr5:74806429-74808097	GM12878	blood:	n/a	chr5:74807423-74807442 chr5:74806850-74806861 chr5:74807425-74807435 chr5:74807425-74807447 chr5:74806737-74806748 chr5:74807422-74807442 chr5:74807426-74807434
25	POLR2A	chr5:74806430-74806946	K562	blood:	n/a	n/a
26	TAF1	chr5:74806800-74808122	A549	lung:	n/a	n/a
27	YY1	chr5:74806722-74808116	GM12878	blood:	n/a	chr5:74807423-74807442 chr5:74806850-74806861 chr5:74807425-74807435 chr5:74807425-74807447 chr5:74806737-74806748 chr5:74807422-74807442 chr5:74807426-74807434
28	POLR2A	chr5:74806884-74808091	HEK293	kidney:	n/a	n/a
29	MAX	chr5:74806446-74808182	ECC-1	luminal epithelium:	n/a	n/a
30	REST	chr5:74806420-74808369	H1-neurons	neurons:	n/a	chr5:74806644-74806657 chr5:74806770-74806779 chr5:74806651-74806660 chr5:74806647-74806660 chr5:74806471-74806491
31	RAD21	chr5:74806435-74808395	IMR90	lung:	n/a	chr5:74807424-74807436 chr5:74807952-74807966
32	TAF1	chr5:74806398-74806958	H1-hESC	embryonic stem cell:	n/a	n/a
33	ZEB1	chr5:74806600-74807046	GM12878	blood:	n/a	chr5:74806892-74806899
34	POLR2A	chr5:74806345-74808532	GM18951	blood:	n/a	n/a
35	MAX	chr5:74806445-74808259	HCT-116	colon:	n/a	n/a
36	SMC3	chr5:74806804-74807126	K562	blood:	n/a	n/a
37	E2F6	chr5:74806641-74806992	K562	blood:	n/a	chr5:74806845-74806856 chr5:74806842-74806851
38	POLR2A	chr5:74806624-74808043	MCF-7	breast:	n/a	n/a
39	TCF12	chr5:74806492-74808039	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr5:74806442-74808012	Hela-S3	cervix:	n/a	n/a
41	SIN3AK20	chr5:74806428-74808154	PANC-1	pancreas:	n/a	n/a
42	TCF7L2	chr5:74806384-74807254	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr5:74806603-74808536	GM12878	blood:	n/a	n/a
44	CHD1	chr5:74805200-74808587	GM12878	blood:	n/a	chr5:74806845-74806855
45	ZKSCAN1	chr5:74806616-74807035	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr5:74806338-74808106	Raji	blood:	n/a	n/a
47	UBTF	chr5:74806470-74808117	K562	blood:	n/a	n/a
48	RAD21	chr5:74806379-74807009	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr5:74806520-74808046	GM12878	blood:	n/a	n/a
50	CREB1	chr5:74806567-74808177	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:74806025..74808781-chr5:74906137..74908952,2	MCF-7	breast:
2	chr5:74804574..74807080-chr5:74963425..74964973,2	K562	blood:
3	chr5:74630713..74633733-chr5:74805590..74808087,5	MCF-7	breast:

Variant related genes	Relation type
POLK	TF binding region
ENSG00000189045	Chromatin interaction
ENSG00000247372	Chromatin interaction
ENSG00000113161	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs17238344	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17238351	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17238358	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17238393	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17244771	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17244778	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17244827	1.00[AMR][1000 genomes]
rs17244876	1.00[AMR][1000 genomes]
rs5744622	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5744697	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5744714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6805	1.00[AMR][1000 genomes]
rs6888071	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882193	chr5:74656175-74917862	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv882195	chr5:74678937-74896798	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv882196	chr5:74678937-74917862	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv882197	chr5:74692776-74946455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv882198	chr5:74736065-74896798	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv882199	chr5:74757758-74946455	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv882200	chr5:74781439-74830808	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	nsv882201	chr5:74787310-74890618	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 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	chr5:74804000-74809000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:74804600-74808600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr5:74804600-74809800	Active TSS	NHLF	lung
4	chr5:74804800-74809600	Active TSS	K562	blood
5	chr5:74805000-74808600	Active TSS	Fetal Stomach	stomach
6	chr5:74805000-74810200	Active TSS	GM12878-XiMat	blood
7	chr5:74805200-74808200	Active TSS	Cortex derived primary cultured neurospheres	brain
8	chr5:74805200-74808400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:74805200-74808400	Active TSS	Brain Cingulate Gyrus	brain
10	chr5:74805200-74808600	Active TSS	HSMMtube	muscle
11	chr5:74805200-74809000	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr5:74805200-74809000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:74805200-74809000	Active TSS	NHDF-Ad	bronchial
14	chr5:74805200-74809400	Active TSS	Right Atrium	heart
15	chr5:74805400-74808200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:74805400-74808400	Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr5:74805400-74808600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:74805400-74808600	Active TSS	Fetal Intestine Large	intestine
19	chr5:74805400-74808600	Active TSS	Right Ventricle	heart
20	chr5:74805400-74808600	Active TSS	HMEC	breast
21	chr5:74805400-74809000	Active TSS	Ovary	ovary
22	chr5:74805400-74809200	Active TSS	HSMM	muscle
23	chr5:74805400-74809400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:74805600-74807000	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr5:74805600-74808200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:74805600-74808200	Active TSS	Rectal Mucosa Donor 31	rectum
27	chr5:74805600-74808400	Active TSS	H1 Cell Line	embryonic stem cell
28	chr5:74805600-74808400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr5:74805600-74808400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr5:74805600-74808400	Active TSS	Fetal Intestine Small	intestine
31	chr5:74805600-74808400	Active TSS	Hela-S3	cervix
32	chr5:74805600-74808600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr5:74805600-74808600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:74805600-74808600	Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr5:74805600-74808600	Active TSS	Muscle Satellite Cultured Cells	--
36	chr5:74805600-74808600	Active TSS	Psoas Muscle	Psoas
37	chr5:74805600-74808800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:74805600-74808800	Active TSS	Aorta	Aorta
39	chr5:74805800-74807000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr5:74805800-74808200	Active TSS	Esophagus	oesophagus
41	chr5:74805800-74808200	Active TSS	Left Ventricle	heart
42	chr5:74805800-74808200	Active TSS	Pancreas	Pancrea
43	chr5:74805800-74808400	Active TSS	H9 Cell Line	embryonic stem cell
44	chr5:74805800-74808400	Active TSS	NHEK	skin
45	chr5:74805800-74808600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr5:74805800-74808600	Active TSS	Colonic Mucosa	Colon
47	chr5:74805800-74808600	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr5:74805800-74808600	Active TSS	Fetal Muscle Trunk	muscle
49	chr5:74805800-74808800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr5:74805800-74808800	Active TSS	Stomach Smooth Muscle	stomach

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