Variant report

Variant	rs152014
Chromosome Location	chr5:96027252-96027253
allele	A/C
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	HNF4A	chr5:96027150-96027459	HepG2	liver:	n/a	chr5:96027280-96027292
2	CEBPB	chr5:96027179-96027936	Hela-S3	cervix:	n/a	chr5:96027770-96027781 chr5:96027770-96027783
3	HNF4A	chr5:96027102-96027494	HepG2	liver:	n/a	chr5:96027280-96027292
4	HNF4A	chr5:96027136-96027480	HepG2	liver:	n/a	chr5:96027280-96027292
5	CTCF	chr5:96027180-96027330	HMEC	breast:	n/a	chr5:96027240-96027258
6	CTCF	chr5:96027200-96027350	WERI-Rb-1	eye:	n/a	chr5:96027240-96027258
7	RAD21	chr5:96027180-96027447	Hela-S3	cervix:	n/a	chr5:96027241-96027260
8	STAT3	chr5:96027219-96027584	MCF10A-Er-Src	breast:	n/a	n/a
9	CTCF	chr5:96027200-96027350	BJ	skin:	n/a	chr5:96027240-96027258
10	CTCF	chr5:96027160-96027310	Caco-2	colon:	n/a	chr5:96027240-96027258
11	FOS	chr5:96026517-96027597	MCF10A-Er-Src	breast:	n/a	chr5:96026804-96026815
12	CTCF	chr5:96027200-96027350	HPAF	blood vessel:	n/a	chr5:96027240-96027258
13	FOS	chr5:96027184-96027558	MCF10A-Er-Src	breast:	n/a	n/a
14	CTCF	chr5:96027204-96027321	Hela-S3	cervix:	n/a	chr5:96027240-96027258
15	CEBPB	chr5:96027181-96027836	HepG2	liver:	n/a	chr5:96027770-96027781 chr5:96027770-96027783
16	POLR2A	chr5:96026850-96027299	MCF10A-Er-Src	breast:	n/a	n/a
17	CTCF	chr5:96027120-96027270	MCF-7	breast:	n/a	chr5:96027240-96027258
18	CTCF	chr5:96027145-96027313	HepG2	liver:	n/a	chr5:96027240-96027258
19	CTCF	chr5:96027224-96027302	MCF-7	breast:	n/a	chr5:96027240-96027258
20	ZEB1	chr5:96027060-96027538	HepG2	liver:	n/a	n/a
21	FOS	chr5:96026551-96027604	MCF10A-Er-Src	breast:	n/a	chr5:96026804-96026815
22	CTCF	chr5:96027200-96027350	HMEC	breast:	n/a	chr5:96027240-96027258
23	RAD21	chr5:96027084-96027390	HepG2	liver:	n/a	chr5:96027241-96027260
24	MYC	chr5:96026555-96027653	MCF10A-Er-Src	breast:	n/a	n/a
25	STAT3	chr5:96027202-96027597	MCF10A-Er-Src	breast:	n/a	n/a
26	FOS	chr5:96027175-96027599	MCF10A-Er-Src	breast:	n/a	n/a
27	CTCF	chr5:96027215-96027294	MCF-7	breast:	n/a	chr5:96027240-96027258
28	CTCF	chr5:96027245-96027267	Kidney_OC	kidney:	n/a	n/a
29	RAD21	chr5:96027153-96027443	HepG2	liver:	n/a	chr5:96027241-96027260
30	ZEB1	chr5:96027120-96027527	HepG2	liver:	n/a	n/a
31	TEAD4	chr5:96027161-96027594	HepG2	liver:	n/a	n/a
32	CTCF	chr5:96027180-96027330	AG09319	gingival:	n/a	chr5:96027240-96027258
33	CEBPB	chr5:96027214-96027484	HepG2	liver:	n/a	n/a
34	RAD21	chr5:96027153-96027390	HepG2	liver:	n/a	chr5:96027241-96027260
35	CTCF	chr5:96027216-96027318	MCF-7	breast:	n/a	chr5:96027240-96027258
36	HNF4G	chr5:96027083-96027542	HepG2	liver:	n/a	chr5:96027279-96027294 chr5:96027280-96027292
37	CTCF	chr5:96027232-96027284	MCF-7	breast:	n/a	chr5:96027240-96027258
38	STAT3	chr5:96027169-96027588	MCF10A-Er-Src	breast:	n/a	n/a
39	MYC	chr5:96027146-96027588	MCF10A-Er-Src	breast:	n/a	n/a
40	CTCF	chr5:96027186-96027313	HepG2	liver:	n/a	chr5:96027240-96027258
41	HNF4G	chr5:96027160-96027473	HepG2	liver:	n/a	chr5:96027279-96027294 chr5:96027280-96027292

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:95930369..95932289-chr5:96026143..96027924,2	K562	blood:

Variant related genes	Relation type
CAST	TF binding region
ENSG00000264129	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10045215	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10067766	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10075736	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1421911	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs151835	1.00[JPT][hapmap]
rs151904	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs152005	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs152017	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs152020	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2351245	0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs26482	0.85[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs26483	0.93[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs26484	0.93[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs26485	0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs26503	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs26504	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs27852	0.93[YRI][hapmap]
rs28040	0.97[ASN][1000 genomes]
rs28093	0.86[JPT][hapmap]
rs28104	0.86[JPT][hapmap]
rs31248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs31249	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs31250	0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4267886	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4590196	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6556937	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6860934	0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6897588	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7704167	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7705824	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7733671	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[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	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs152014	CTC-506B8.1	cis	Whole Blood	GTEx
rs152014	CAST	cis	lung	GTEx
rs152014	CAST	cis	Esophagus Muscularis	GTEx
rs152014	CTC-506B8.1	cis	Adipose Subcutaneous	GTEx
rs152014	CAST	cis	Artery Tibial	GTEx
rs152014	CAST	cis	Nerve Tibial	GTEx
rs152014	CAST	Cis_1M	lymphoblastoid	RTeQTL
rs152014	CTC-506B8.1	cis	Artery Tibial	GTEx
rs152014	CAST	cis	Adipose Subcutaneous	GTEx
rs152014	CAST	cis	Whole Blood	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95999400-96038000	Weak transcription	Fetal Stomach	stomach
2	chr5:95999600-96028200	Weak transcription	Aorta	Aorta
3	chr5:95999600-96037800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr5:95999600-96038000	Weak transcription	Fetal Lung	lung
5	chr5:96000800-96037600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr5:96001600-96037000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr5:96002400-96027800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr5:96002400-96037600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr5:96002400-96038200	Weak transcription	Esophagus	oesophagus
10	chr5:96004800-96028200	Weak transcription	Lung	lung
11	chr5:96004800-96036600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr5:96005000-96038000	Weak transcription	Ovary	ovary
13	chr5:96005000-96038200	Weak transcription	Gastric	stomach
14	chr5:96005600-96027800	Weak transcription	Left Ventricle	heart
15	chr5:96007600-96027800	Weak transcription	Fetal Intestine Large	intestine
16	chr5:96009200-96037600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr5:96013000-96037800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr5:96013600-96031400	Weak transcription	Stomach Mucosa	stomach
19	chr5:96013800-96037600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:96014000-96030800	Weak transcription	HSMM	muscle
21	chr5:96014800-96027400	Weak transcription	Fetal Intestine Small	intestine
22	chr5:96015400-96031800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr5:96016200-96031600	Weak transcription	Fetal Muscle Leg	muscle
24	chr5:96016600-96035200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr5:96016800-96027800	Weak transcription	Right Atrium	heart
26	chr5:96016800-96035000	Weak transcription	Brain Hippocampus Middle	brain
27	chr5:96016800-96038200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr5:96017000-96034000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr5:96017000-96038000	Weak transcription	Colon Smooth Muscle	Colon
30	chr5:96017200-96027600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:96018800-96038200	Weak transcription	Colonic Mucosa	Colon
32	chr5:96018800-96038200	Weak transcription	Spleen	Spleen
33	chr5:96019000-96031600	Weak transcription	Fetal Muscle Trunk	muscle
34	chr5:96019400-96031600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr5:96021800-96027800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr5:96021800-96032000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr5:96022200-96031600	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr5:96022200-96034800	Weak transcription	NH-A	brain
39	chr5:96022400-96031600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr5:96023000-96027800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr5:96023000-96030400	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr5:96023000-96035000	Weak transcription	Right Ventricle	heart
43	chr5:96023000-96038400	Weak transcription	Small Intestine	intestine
44	chr5:96023200-96037600	Weak transcription	Thymus	Thymus
45	chr5:96023400-96031200	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr5:96023400-96032000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr5:96023600-96031200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr5:96023600-96033000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr5:96023600-96035000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr5:96023600-96036800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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