Variant report

Variant	rs5030515
Chromosome Location	chr4:110625121-110625122
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	POLR2A	chr4:110623065-110625373	GM12891	blood:	n/a	n/a
2	POLR2A	chr4:110622699-110625610	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr4:110624089-110625161	MCF-7	breast:	n/a	n/a
4	POLR2A	chr4:110624091-110625314	K562	blood:	n/a	n/a
5	POLR2A	chr4:110624119-110625134	HCT-116	colon:	n/a	n/a
6	MAZ	chr4:110623824-110625166	GM12878	blood:	n/a	n/a
7	NFATC1	chr4:110624366-110625157	GM12878	blood:	n/a	n/a
8	SMC3	chr4:110623776-110625919	SK-N-SH	brain:	n/a	chr4:110624276-110624290 chr4:110624280-110624290
9	POLR2A	chr4:110624082-110625147	Hela-S3	cervix:	n/a	n/a
10	STAT3	chr4:110625111-110625385	MCF10A-Er-Src	breast:	n/a	chr4:110625278-110625289
11	POLR2A	chr4:110624045-110625405	K562	blood:	n/a	n/a
12	POLR2A	chr4:110623853-110625277	K562	blood:	n/a	n/a
13	POLR2A	chr4:110623848-110625598	Hela-S3	cervix:	n/a	n/a
14	EP300	chr4:110625082-110625479	SK-N-SH_RA	brain:	n/a	n/a
15	POLR2A	chr4:110623739-110625267	MCF10A-Er-Src	breast:	n/a	n/a
16	RCOR1	chr4:110624090-110625181	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr4:110623756-110625130	PBDE	blood:	n/a	n/a
18	POLR2A	chr4:110623968-110625156	HUVEC	blood vessel:	n/a	n/a
19	EP300	chr4:110625097-110625457	SK-N-SH_RA	brain:	n/a	n/a
20	CEBPB	chr4:110624138-110625209	Hela-S3	cervix:	n/a	chr4:110625084-110625095
21	STAT3	chr4:110625094-110625420	MCF10A-Er-Src	breast:	n/a	chr4:110625278-110625289
22	POLR2A	chr4:110624016-110625543	SK-N-MC	brain:	n/a	n/a
23	POLR2A	chr4:110623806-110625220	SK-N-MC	brain:	n/a	n/a
24	POLR2A	chr4:110623957-110625264	K562	blood:	n/a	n/a
25	SIN3AK20	chr4:110623812-110625138	MCF-7	breast:	n/a	n/a
26	TFAP2C	chr4:110623911-110625163	Hela-S3	cervix:	n/a	chr4:110624831-110624846 chr4:110624802-110624817
27	CEBPB	chr4:110625026-110625226	K562	blood:	n/a	chr4:110625084-110625095
28	MAZ	chr4:110624000-110625313	K562	blood:	n/a	n/a
29	RAD21	chr4:110625094-110625464	SK-N-SH_RA	brain:	n/a	n/a
30	HA-E2F1	chr4:110623827-110625144	MCF-7	breast:	n/a	chr4:110624251-110624261 chr4:110624322-110624331 chr4:110624323-110624330 chr4:110624323-110624330 chr4:110624323-110624330 chr4:110624687-110624696 chr4:110624777-110624787 chr4:110624252-110624262
31	POLR2A	chr4:110622902-110625466	GM12878	blood:	n/a	n/a
32	E2F4	chr4:110623616-110625162	MCF10A-Er-Src	breast:	n/a	chr4:110624251-110624261 chr4:110624322-110624331 chr4:110624323-110624330 chr4:110624323-110624330 chr4:110624323-110624330 chr4:110624687-110624696 chr4:110624777-110624787 chr4:110624252-110624262
33	EBF1	chr4:110623138-110625419	GM12878	blood:	n/a	chr4:110624832-110624843
34	MTA3	chr4:110623730-110625188	GM12878	blood:	n/a	n/a
35	PBX3	chr4:110625053-110625616	SK-N-SH	brain:	n/a	n/a
36	TFAP2A	chr4:110623900-110625140	Hela-S3	cervix:	n/a	chr4:110624881-110624891 chr4:110624032-110624044 chr4:110624879-110624893 chr4:110624879-110624893 chr4:110624879-110624893 chr4:110624881-110624891 chr4:110624831-110624846 chr4:110624881-110624891 chr4:110624881-110624891
37	POLR2A	chr4:110624111-110625441	PFSK-1	brain:	n/a	n/a
38	ARID3A	chr4:110625108-110625369	K562	blood:	n/a	n/a
39	MAZ	chr4:110622909-110625527	IMR90	lung:	n/a	chr4:110623059-110623069
40	POLR2A	chr4:110623773-110633628	K562	blood:	n/a	n/a
41	CCNT2	chr4:110623675-110625184	K562	blood:	n/a	n/a
42	STAT3	chr4:110625096-110625439	MCF10A-Er-Src	breast:	n/a	chr4:110625278-110625289
43	POLR2A	chr4:110624179-110625278	K562	blood:	n/a	n/a
44	POLR2A	chr4:110623816-110625163	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:110625080-110625130	NH-A	brain:	n/a
2	chr4:110625080-110625130	K562	blood:	n/a
3	chr4:110625080-110625130	HUVEC	blood vessel:	n/a
4	chr4:110625080-110625130	NT2-D1	testis:	n/a
5	chr4:110625080-110625130	GM12892	blood:	n/a
6	chr4:110625080-110625130	AG04450	lung:	fetal
7	chr4:110625080-110625130	LNCaP	prostate:	n/a
8	chr4:110625080-110625130	ECC-1	luminal epithelium:	n/a
9	chr4:110625080-110625130	AoSMC	blood vessel:	n/a
10	chr4:110625080-110625130	SK-N-SH	brain:	n/a
11	chr4:110625080-110625130	BE2_C	brain:	n/a
12	chr4:110625080-110625130	PANC-1	pancreas:	n/a
13	chr4:110625080-110625130	IMR90	lung:	fetal
14	chr4:110625080-110625130	NB4	blood:	n/a
15	chr4:110625080-110625130	HCPEpiC	choroid plexus:	n/a
16	chr4:110625080-110625130	GM12878	blood:	n/a
17	chr4:110625080-110625130	GM19239	blood:	n/a
18	chr4:110625080-110625130	SKMC	muscle:	n/a
19	chr4:110625080-110625130	Hela-S3	cervix:	n/a
20	chr4:110625080-110625130	HCM	heart:	n/a
21	chr4:110625080-110625130	SK-N-SH_RA	brain:	n/a
22	chr4:110625080-110625130	HNPCEpiC	eye:	n/a
23	chr4:110625080-110625130	HIPEpiC	eye:	n/a
24	chr4:110625080-110625130	HAEpiC	amniotic membrane:	n/a
25	chr4:110625080-110625130	HRPEpiC	eye:	n/a
26	chr4:110625080-110625130	HEEpiC	esophagus:	n/a
27	chr4:110625080-110625130	PFSK-1	brain:	n/a
28	chr4:110625080-110625130	AG10803	skin:	n/a
29	chr4:110625080-110625130	SAEC	small airway:	n/a
30	chr4:110625080-110625130	GM06990	blood:	n/a
31	chr4:110625080-110625130	U87	brain:	n/a
32	chr4:110625080-110625130	A549	lung:	n/a
33	chr4:110625080-110625130	Hepatocyte	liver:	n/a
34	chr4:110625080-110625130	Caco-2	colon:	n/a
35	chr4:110625080-110625130	H1-hESC	embryonic stem cell:	embryo
36	chr4:110625080-110625130	ProgFib	skin:	n/a
37	chr4:110625080-110625130	HRE	kidney:	n/a
38	chr4:110625080-110625130	Jurkat	blood:	n/a
39	chr4:110625080-110625130	MCF-7	breast:	n/a
40	chr4:110625080-110625130	RPTEC	kidney:	n/a
41	chr4:110625080-110625130	GM12891	blood:	n/a
42	chr4:110625080-110625130	PrEC	prostate:	n/a
43	chr4:110625080-110625130	HMEC	breast:	n/a
44	chr4:110625080-110625130	HCT-116	colon:	n/a
45	chr4:110625080-110625130	AG04449	skin:	fetal
46	chr4:110625080-110625130	HL-60	blood:	n/a
47	chr4:110625080-110625130	BJ	skin:	n/a
48	chr4:110625080-110625130	CMK	blood:	n/a
49	chr4:110625080-110625130	HCF	heart:	n/a
50	chr4:110625080-110625130	MCF10A-Er-Src	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:110622125..110626663-chr4:110647059..110653148,13	MCF-7	breast:
2	chr4:110621753..110625851-chr4:110723328..110725382,3	MCF-7	breast:
3	chr4:110623968..110625956-chr4:110651024..110652981,2	MCF-7	breast:
4	chr4:110618563..110622220-chr4:110622548..110625878,6	K562	blood:
5	chr4:110622297..110625771-chr4:110735143..110738902,5	K562	blood:
6	chr4:110623136..110625842-chr4:110784972..110787630,2	MCF-7	breast:

Variant related genes	Relation type
CASP6	TF binding region
CASP6	CpG island
ENSG00000138794	Chromatin interaction
ENSG00000183423	Chromatin interaction
ENSG00000205403	Chromatin interaction
ENSG00000272795	Chromatin interaction
ENSG00000123739	Chromatin interaction
ENSG00000109534	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs5030546	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5030548	1.00[EUR][1000 genomes]
rs5030581	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6830168	1.00[AMR][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	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv595142	chr4:110609481-110656730	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 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	chr4:110622800-110625200	Active TSS	H9 Cell Line	embryonic stem cell
2	chr4:110622800-110625200	Active TSS	Fetal Intestine Large	intestine
3	chr4:110623000-110625200	Active TSS	Fetal Kidney	kidney
4	chr4:110623000-110625200	Active TSS	NH-A	brain
5	chr4:110623200-110625200	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr4:110623200-110625200	Active TSS	H1 Cell Line	embryonic stem cell
7	chr4:110623200-110625400	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr4:110623200-110625400	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr4:110623400-110625200	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr4:110623400-110625200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:110623400-110625200	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr4:110623400-110625200	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr4:110623400-110625200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:110623400-110625200	Active TSS	Ovary	ovary
15	chr4:110623400-110625200	Active TSS	Rectal Smooth Muscle	rectum
16	chr4:110623400-110625200	Active TSS	Right Ventricle	heart
17	chr4:110623400-110625200	Active TSS	NHDF-Ad	bronchial
18	chr4:110623400-110625400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:110623400-110625400	Active TSS	Colonic Mucosa	Colon
20	chr4:110623400-110625400	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr4:110623400-110625400	Active TSS	Right Atrium	heart
22	chr4:110623400-110625400	Active TSS	Stomach Mucosa	stomach
23	chr4:110623600-110625200	Active TSS	Muscle Satellite Cultured Cells	--
24	chr4:110623600-110625200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:110623600-110625400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:110623600-110625400	Active TSS	Duodenum Mucosa	Duodenum
27	chr4:110623600-110625400	Active TSS	Osteobl	bone
28	chr4:110623800-110625200	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr4:110623800-110625200	Active TSS	Fetal Muscle Leg	muscle
30	chr4:110623800-110625200	Active TSS	Fetal Thymus	thymus
31	chr4:110623800-110625400	Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr4:110623800-110625400	Active TSS	Fetal Muscle Trunk	muscle
33	chr4:110623800-110625400	Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr4:110624600-110625200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr4:110624600-110625200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr4:110624600-110625200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr4:110624600-110625200	Flanking Active TSS	Dnd41	blood
38	chr4:110624600-110625400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:110624600-110625400	Active TSS	Brain Germinal Matrix	brain
40	chr4:110624600-110637000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr4:110624800-110625200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:110624800-110625200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr4:110624800-110625200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr4:110624800-110625200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr4:110624800-110625200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:110624800-110625200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:110624800-110625200	Flanking Active TSS	Primary B cells from peripheral blood	blood
48	chr4:110624800-110625200	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr4:110624800-110625200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
50	chr4:110624800-110625200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

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