Variant report

Variant	rs6877508
Chromosome Location	chr5:58572001-58572002
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	TAF1	chr5:58571025-58572208	PFSK-1	brain:	n/a	n/a
2	RFX5	chr5:58571631-58572181	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr5:58570169-58572235	PFSK-1	brain:	n/a	n/a
4	BCL3	chr5:58571625-58572242	A549	lung:	n/a	chr5:58572112-58572121
5	GATA3	chr5:58571556-58572051	T-47D	breast:	n/a	n/a
6	TCF12	chr5:58570995-58573403	A549	lung:	n/a	n/a
7	EP300	chr5:58571295-58572311	A549	lung:	n/a	chr5:58571497-58571511 chr5:58571638-58571652
8	SIN3AK20	chr5:58571221-58572270	A549	lung:	n/a	n/a
9	EP300	chr5:58571156-58572385	A549	lung:	n/a	chr5:58571497-58571511 chr5:58571638-58571652
10	FOS	chr5:58571813-58572110	MCF10A-Er-Src	breast:	n/a	n/a
11	GATA3	chr5:58571048-58573456	A549	lung:	n/a	chr5:58572097-58572107
12	POLR2A	chr5:58571651-58572156	HUVEC	blood vessel:	n/a	n/a
13	CEBPB	chr5:58571414-58572351	Hela-S3	cervix:	n/a	n/a
14	MAX	chr5:58571118-58572215	A549	lung:	n/a	n/a
15	FOSL2	chr5:58571388-58572376	A549	lung:	n/a	chr5:58571647-58571656
16	SP1	chr5:58571254-58572212	A549	lung:	n/a	chr5:58572021-58572028
17	POLR2A	chr5:58571942-58572049	A549	lung:	n/a	n/a
18	TCF7L2	chr5:58571828-58572129	Hela-S3	cervix:	n/a	n/a
19	SIN3AK20	chr5:58571059-58572187	PFSK-1	brain:	n/a	n/a
20	MYC	chr5:58571878-58572064	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr5:58571618-58572192	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr5:58571312-58572306	MCF10A-Er-Src	breast:	n/a	n/a
23	GATA3	chr5:58571585-58572141	T-47D	breast:	n/a	chr5:58572097-58572107
24	POLR2A	chr5:58571971-58572081	A549	lung:	n/a	n/a
25	POLR2A	chr5:58571220-58572326	Hela-S3	cervix:	n/a	n/a
26	MAFK	chr5:58571916-58572297	Hela-S3	cervix:	n/a	n/a
27	STAT3	chr5:58571909-58572066	MCF10A-Er-Src	breast:	n/a	n/a
28	REST	chr5:58571102-58572394	A549	lung:	n/a	chr5:58571726-58571739 chr5:58571372-58571385
29	POLR2A	chr5:58571182-58572262	HUVEC	blood vessel:	n/a	n/a
30	SIN3AK20	chr5:58571232-58572174	PFSK-1	brain:	n/a	n/a
31	TCF7L2	chr5:58571453-58572378	HEK293	kidney:	n/a	n/a
32	ZNF384	chr5:58571946-58572118	GM12878	blood:	n/a	n/a
33	POLR2A	chr5:58571233-58572193	PFSK-1	brain:	n/a	n/a
34	POLR2A	chr5:58571211-58573626	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr5:58571940-58572055	A549	lung:	n/a	n/a
36	SP1	chr5:58570680-58572402	A549	lung:	n/a	chr5:58572021-58572028
37	TBP	chr5:58571148-58573227	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr5:58571677-58572190	Hela-S3	cervix:	n/a	n/a
39	CTCF	chr5:58571920-58572070	WI-38	lung:	n/a	n/a
40	POLR2A	chr5:58570997-58573240	Hela-S3	cervix:	n/a	n/a
41	TFAP2C	chr5:58571545-58572095	Hela-S3	cervix:	n/a	n/a
42	BCL3	chr5:58571142-58572087	A549	lung:	n/a	chr5:58571374-58571383
43	GTF2F1	chr5:58571397-58572116	Hela-S3	cervix:	n/a	n/a
44	KAP1	chr5:58571171-58572338	HEK293	kidney:	n/a	n/a
45	RAD21	chr5:58571745-58572045	Hela-S3	cervix:	n/a	chr5:58571929-58571941
46	KAP1	chr5:58571328-58572345	U2OS	brain:	n/a	n/a
47	FOS	chr5:58571808-58572099	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:7052647..7053265-chr5:58571726..58572393,2	Hela-S3	cervix:
2	chr17:59327949..59328466-chr5:58571972..58572886,2	Hela-S3	cervix:

Variant related genes	Relation type
PDE4D	TF binding region
ENSG00000238923	Chromatin interaction
ENSG00000111678	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1031197	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10491352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10940644	0.84[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs11954668	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11959132	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs11959567	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12189022	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12518773	0.97[ASN][1000 genomes]
rs12519611	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12521263	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12522944	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1445948	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1445952	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1445953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1445954	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1579848	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1579849	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16889479	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16889499	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16889518	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17444185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17528522	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17528578	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17628114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17780175	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1823070	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1838733	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1840846	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1867711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1867712	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1947090	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1947095	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2013979	0.81[CHD][hapmap]
rs2021775	1.00[JPT][hapmap]
rs2028836	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2081106	1.00[JPT][hapmap]
rs2409631	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4700325	1.00[JPT][hapmap]
rs4700328	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6858946	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6888028	0.81[ASN][1000 genomes]
rs6891161	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7443333	0.93[GIH][hapmap]
rs7703022	1.00[CHB][hapmap];0.89[CHD][hapmap]
rs7717303	0.81[ASN][1000 genomes]
rs7719441	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598252	chr5:58487764-58618889	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6877508	PLK2	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58567400-58572200	Active TSS	A549	lung
2	chr5:58568200-58572800	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr5:58568200-58572800	Active TSS	Stomach Smooth Muscle	stomach
4	chr5:58568600-58572200	Active TSS	Fetal Muscle Trunk	muscle
5	chr5:58568600-58572400	Active TSS	Fetal Muscle Leg	muscle
6	chr5:58568600-58572600	Active TSS	Hela-S3	cervix
7	chr5:58569000-58572200	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr5:58569000-58572200	Active TSS	Fetal Intestine Large	intestine
9	chr5:58569200-58572200	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr5:58569200-58572400	Active TSS	Rectal Mucosa Donor 31	rectum
11	chr5:58569400-58572200	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr5:58569800-58572200	Active TSS	Fetal Stomach	stomach
13	chr5:58570000-58572200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr5:58570000-58572200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr5:58570000-58572400	Active TSS	Right Atrium	heart
16	chr5:58570200-58572200	Active TSS	Brain Anterior Caudate	brain
17	chr5:58570200-58572200	Active TSS	Brain Hippocampus Middle	brain
18	chr5:58570200-58572400	Active TSS	Duodenum Mucosa	Duodenum
19	chr5:58570200-58572400	Active TSS	Fetal Intestine Small	intestine
20	chr5:58570600-58572200	Active TSS	Fetal Lung	lung
21	chr5:58570600-58572600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:58570800-58572200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:58570800-58572200	Active TSS	Brain Substantia Nigra	brain
24	chr5:58570800-58572200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr5:58570800-58572200	Active TSS	HMEC	breast
26	chr5:58570800-58572400	Active TSS	Osteobl	bone
27	chr5:58571000-58572200	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr5:58571000-58572200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr5:58571000-58572200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr5:58571000-58572200	Active TSS	Aorta	Aorta
31	chr5:58571000-58572200	Active TSS	NHDF-Ad	bronchial
32	chr5:58571000-58573800	Enhancers	Fetal Heart	heart
33	chr5:58571200-58572200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:58571200-58572200	Enhancers	Primary B cells from peripheral blood	blood
35	chr5:58571200-58572200	Active TSS	Pancreas	Pancrea
36	chr5:58571200-58572200	Active TSS	HSMM	muscle
37	chr5:58571200-58572200	Active TSS	HSMMtube	muscle
38	chr5:58571200-58572400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr5:58571400-58572200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr5:58571400-58572200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
41	chr5:58571400-58572200	Active TSS	Thymus	Thymus
42	chr5:58571400-58572400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr5:58571400-58572400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr5:58571600-58572200	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr5:58571600-58572200	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr5:58571600-58572200	Active TSS	NHEK	skin
47	chr5:58571600-58572200	Flanking Active TSS	NHLF	lung
48	chr5:58571600-58572400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr5:58571600-58572400	Flanking Active TSS	HUVEC	blood vessel
50	chr5:58571600-58572400	Active TSS	NH-A	brain

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