Variant report

Variant	rs9484678
Chromosome Location	chr6:143267609-143267610
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	POLR2A	chr6:143265481-143268845	Hela-S3	cervix:	n/a	n/a
2	TCF12	chr6:143267496-143267834	GM12878	blood:	n/a	n/a
3	SP1	chr6:143267377-143267818	H1-hESC	embryonic stem cell:	n/a	n/a
4	CHD1	chr6:143267499-143268438	H1-hESC	embryonic stem cell:	n/a	chr6:143267979-143267989 chr6:143267725-143267735 chr6:143268285-143268295
5	MAX	chr6:143267261-143267753	K562	blood:	n/a	n/a
6	PAX5	chr6:143267396-143267843	GM12878	blood:	n/a	chr6:143267739-143267748
7	ZNF143	chr6:143266941-143268279	H1-hESC	embryonic stem cell:	n/a	chr6:143267660-143267678
8	CREB1	chr6:143267286-143267884	H1-hESC	embryonic stem cell:	n/a	n/a
9	STAT3	chr6:143267263-143268024	MCF10A-Er-Src	breast:	n/a	chr6:143267869-143267881 chr6:143267459-143267470
10	POLR2A	chr6:143266612-143268022	ProgFib	skin:	n/a	n/a
11	RELA	chr6:143267464-143269260	GM18505	blood:	n/a	n/a
12	POLR2A	chr6:143264681-143268850	NB4	blood:	n/a	n/a
13	YY1	chr6:143267314-143267780	ECC-1	luminal epithelium:	n/a	chr6:143267355-143267366 chr6:143267349-143267360 chr6:143267711-143267722 chr6:143267415-143267429
14	MYBL2	chr6:143267313-143267965	HepG2	liver:	n/a	n/a
15	POLR2A	chr6:143266644-143267876	HCT-116	colon:	n/a	n/a
16	SP1	chr6:143267401-143267826	A549	lung:	n/a	n/a
17	MAZ	chr6:143267342-143267886	K562	blood:	n/a	n/a
18	POLR2A	chr6:143267542-143267790	A549	lung:	n/a	n/a
19	MAX	chr6:143266713-143268344	Hela-S3	cervix:	n/a	chr6:143267986-143267996
20	STAT5A	chr6:143266953-143267987	GM12878	blood:	n/a	chr6:143267869-143267881 chr6:143267002-143267014
21	REST	chr6:143267375-143267742	ECC-1	luminal epithelium:	n/a	n/a
22	FOXM1	chr6:143266943-143268385	GM12878	blood:	n/a	n/a
23	EGR1	chr6:143267394-143267769	GM12878	blood:	n/a	chr6:143267505-143267518 chr6:143267543-143267557
24	SIN3AK20	chr6:143267292-143267953	H1-hESC	embryonic stem cell:	n/a	n/a
25	ATF2	chr6:143267329-143267849	H1-hESC	embryonic stem cell:	n/a	chr6:143267566-143267580
26	SPI1	chr6:143267369-143267707	GM12878	blood:	n/a	n/a
27	TEAD4	chr6:143267302-143268196	ECC-1	luminal epithelium:	n/a	n/a
28	MYC	chr6:143267485-143267620	HUVEC	blood vessel:	n/a	n/a
29	EP300	chr6:143267370-143267844	T-47D	breast:	n/a	chr6:143267715-143267731
30	YY1	chr6:143266614-143267767	GM12878	blood:	n/a	chr6:143267355-143267366 chr6:143267349-143267360 chr6:143267060-143267074 chr6:143266881-143266890 chr6:143266875-143266889 chr6:143266981-143266992 chr6:143267711-143267722 chr6:143267415-143267429 chr6:143266984-143266993
31	JUND	chr6:143267359-143267844	HepG2	liver:	n/a	n/a
32	TCF12	chr6:143267456-143267751	H1-hESC	embryonic stem cell:	n/a	chr6:143267460-143267468
33	MAX	chr6:143267062-143269246	GM12878	blood:	n/a	chr6:143267986-143267996
34	POLR2A	chr6:143264900-143269271	GM18505	blood:	n/a	n/a
35	ZBTB7A	chr6:143267362-143268007	ECC-1	luminal epithelium:	n/a	chr6:143267982-143267991
36	RCOR1	chr6:143264937-143269025	HepG2	liver:	n/a	n/a
37	CREB1	chr6:143267409-143267751	A549	lung:	n/a	n/a
38	YY1	chr6:143267294-143267846	SK-N-SH_RA	brain:	n/a	chr6:143267355-143267366 chr6:143267349-143267360 chr6:143267711-143267722 chr6:143267415-143267429
39	POLR2A	chr6:143266503-143267915	MCF-7	breast:	n/a	n/a
40	ATF2	chr6:143267299-143269472	GM12878	blood:	n/a	chr6:143267566-143267580
41	RAD21	chr6:143267510-143267671	HepG2	liver:	n/a	n/a
42	MTA3	chr6:143267217-143268524	GM12878	blood:	n/a	n/a
43	JUND	chr6:143267066-143267990	H1-hESC	embryonic stem cell:	n/a	n/a
44	EP300	chr6:143267347-143269059	HepG2	liver:	n/a	chr6:143268890-143268904 chr6:143267715-143267731 chr6:143267355-143267364
45	POLR2A	chr6:143264910-143269253	GM12892	blood:	n/a	n/a
46	ATF2	chr6:143267338-143268249	H1-hESC	embryonic stem cell:	n/a	chr6:143267566-143267580
47	TCF3	chr6:143267300-143267793	GM12878	blood:	n/a	chr6:143267392-143267406
48	POLR2A	chr6:143267279-143268301	A549	lung:	n/a	n/a
49	POU2F2	chr6:143267411-143268987	GM12891	blood:	n/a	chr6:143267425-143267437 chr6:143267721-143267733 chr6:143268170-143268182 chr6:143268551-143268563
50	UBTF	chr6:143267296-143267893	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:143267593-143267643	GM12878	blood:	n/a
2	chr6:143267593-143267643	GM12892	blood:	n/a
3	chr6:143267593-143267643	HL-60	blood:	n/a
4	chr6:143267593-143267643	LNCaP	prostate:	n/a
5	chr6:143267593-143267643	Caco-2	colon:	n/a
6	chr6:143267593-143267643	GM06990	blood:	n/a
7	chr6:143267593-143267643	NB4	blood:	n/a
8	chr6:143267593-143267643	HAEpiC	amniotic membrane:	n/a
9	chr6:143267593-143267643	H1-hESC	embryonic stem cell:	embryo
10	chr6:143267593-143267643	MCF-7	breast:	n/a
11	chr6:143267593-143267643	AG09319	gingival:	n/a
12	chr6:143267593-143267643	HEK293	kidney:	embryo
13	chr6:143267593-143267643	Jurkat	blood:	n/a
14	chr6:143267593-143267643	HCF	heart:	n/a
15	chr6:143267593-143267643	Hela-S3	cervix:	n/a
16	chr6:143267593-143267643	HEEpiC	esophagus:	n/a
17	chr6:143267593-143267643	GM12891	blood:	n/a
18	chr6:143267593-143267643	PANC-1	pancreas:	n/a
19	chr6:143267593-143267643	ovcar-3	ovarian:	n/a
20	chr6:143267593-143267643	AoSMC	blood vessel:	n/a
21	chr6:143267593-143267643	HRCEpiC	kidney:	n/a
22	chr6:143267593-143267643	HepG2	liver:	n/a
23	chr6:143267593-143267643	AG04450	lung:	fetal
24	chr6:143267593-143267643	HCM	heart:	n/a
25	chr6:143267593-143267643	BJ	skin:	n/a
26	chr6:143267593-143267643	NHBE	bronchial:	n/a
27	chr6:143267593-143267643	PFSK-1	brain:	n/a
28	chr6:143267593-143267643	AG10803	skin:	n/a
29	chr6:143267593-143267643	NT2-D1	testis:	n/a
30	chr6:143267593-143267643	AG09309	skin:	n/a
31	chr6:143267593-143267643	GM19239	blood:	n/a
32	chr6:143267593-143267643	HPAEpiC	pulmonary alveolar:	n/a
33	chr6:143267593-143267643	HNPCEpiC	eye:	n/a
34	chr6:143267593-143267643	ProgFib	skin:	n/a
35	chr6:143267593-143267643	U87	brain:	n/a
36	chr6:143267593-143267643	HCPEpiC	choroid plexus:	n/a
37	chr6:143267593-143267643	SKMC	muscle:	n/a
38	chr6:143267593-143267643	T-47D	breast:	n/a
39	chr6:143267593-143267643	BE2_C	brain:	n/a
40	chr6:143267593-143267643	SK-N-SH	brain:	n/a
41	chr6:143267593-143267643	PrEC	prostate:	n/a
42	chr6:143267593-143267643	A549	lung:	n/a
43	chr6:143267593-143267643	SK-N-SH_RA	brain:	n/a
44	chr6:143267593-143267643	HRPEpiC	eye:	n/a
45	chr6:143267593-143267643	SAEC	small airway:	n/a
46	chr6:143267593-143267643	ECC-1	luminal epithelium:	n/a
47	chr6:143267593-143267643	IMR90	lung:	fetal
48	chr6:143267593-143267643	K562	blood:	n/a
49	chr6:143267593-143267643	MCF10A-Er-Src	breast:	n/a
50	chr6:143267593-143267643	HIPEpiC	eye:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:143167088..143169502-chr6:143267608..143269824,2	MCF-7	breast:
2	chr17:56708877..56709444-chr6:143267554..143268195,2	HCT-116	colon:
3	chr6:143264696..143268807-chr6:143380557..143382998,8	MCF-7	breast:
4	chr6:143267204..143268811-chr6:143547362..143549725,2	MCF-7	breast:
5	chr6:143266356..143269591-chr6:143770736..143773354,3	MCF-7	breast:
6	chr6:143266456..143269771-chr6:143270572..143274833,7	MCF-7	breast:
7	chr20:55771251..55773542-chr6:143266814..143269705,2	MCF-7	breast:
8	chr6:143068612..143070141-chr6:143265805..143267834,2	MCF-7	breast:
9	chr12:54752780..54753432-chr6:143267604..143268313,2	Hela-S3	cervix:
10	chr6:143267072..143267718-chr9:130953877..130954724,2	Hela-S3	cervix:
11	chr6:143266471..143269313-chr6:143346682..143349454,3	MCF-7	breast:
12	chr6:143156192..143158401-chr6:143265953..143267807,2	MCF-7	breast:

Variant related genes	Relation type
HIVEP2	TF binding region
ENSG00000232618	TF binding region
HIVEP2	CpG island
ENSG00000232618	CpG island
ENSG00000189007	Chromatin interaction
ENSG00000233138	Chromatin interaction
ENSG00000034693	Chromatin interaction
ENSG00000146416	Chromatin interaction
ENSG00000010818	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000148337	Chromatin interaction
ENSG00000232618	Chromatin interaction
ENSG00000223203	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs59123279	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73588423	0.83[AMR][1000 genomes]
rs73588427	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7766704	1.00[AMR][1000 genomes]
rs7768273	0.83[AMR][1000 genomes]
rs9484679	0.85[AFR][1000 genomes]
rs9496484	1.00[AMR][1000 genomes]
rs9496485	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv538459	chr6:143165802-143360098	Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 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	chr6:143262600-143269400	Active TSS	Fetal Brain Female	brain
2	chr6:143263600-143269600	Active TSS	Thymus	Thymus
3	chr6:143263800-143269400	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr6:143264200-143269200	Active TSS	GM12878-XiMat	blood
5	chr6:143264200-143269400	Active TSS	Psoas Muscle	Psoas
6	chr6:143264400-143269200	Active TSS	Rectal Smooth Muscle	rectum
7	chr6:143264600-143269200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:143264600-143269400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:143264600-143269600	Active TSS	Brain Angular Gyrus	brain
10	chr6:143264800-143268800	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr6:143264800-143269000	Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr6:143264800-143269200	Active TSS	H1 Cell Line	embryonic stem cell
13	chr6:143264800-143269200	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr6:143264800-143269400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr6:143264800-143269400	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr6:143264800-143269400	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr6:143264800-143269600	Active TSS	Brain Anterior Caudate	brain
18	chr6:143265000-143268000	Active TSS	Fetal Muscle Trunk	muscle
19	chr6:143265000-143269000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:143265000-143269000	Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr6:143265000-143269000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:143265000-143269000	Active TSS	Colon Smooth Muscle	Colon
23	chr6:143265000-143269000	Active TSS	HMEC	breast
24	chr6:143265000-143269200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:143265000-143269200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:143265000-143269200	Active TSS	Aorta	Aorta
27	chr6:143265000-143269200	Active TSS	Colonic Mucosa	Colon
28	chr6:143265000-143269200	Active TSS	Lung	lung
29	chr6:143265000-143269200	Active TSS	Ovary	ovary
30	chr6:143265000-143269200	Active TSS	Right Atrium	heart
31	chr6:143265000-143269400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:143265000-143269400	Active TSS	NHLF	lung
33	chr6:143265200-143268600	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr6:143265200-143268800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr6:143265200-143268800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr6:143265200-143268800	Active TSS	Gastric	stomach
37	chr6:143265200-143268800	Active TSS	NHEK	skin
38	chr6:143265200-143269000	Active TSS	Small Intestine	intestine
39	chr6:143265200-143269200	Active TSS	H9 Cell Line	embryonic stem cell
40	chr6:143265200-143269200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:143265200-143269200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:143265200-143269200	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr6:143265200-143269200	Active TSS	Brain Cingulate Gyrus	brain
44	chr6:143265200-143269200	Active TSS	Right Ventricle	heart
45	chr6:143265200-143269400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:143265400-143267800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:143265400-143267800	Active TSS	Primary T cells fromperipheralblood	blood
48	chr6:143265400-143267800	Active TSS	Fetal Muscle Leg	muscle
49	chr6:143265400-143267800	Active TSS	Fetal Thymus	thymus
50	chr6:143265400-143268000	Active TSS	Fetal Adrenal Gland	Adrenal Gland

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