Variant report

Variant	rs9296478
Chromosome Location	chr6:46097406-46097407
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:72)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:72 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT1	chr6:46097271-46098205	GM12878	blood:	n/a	n/a
2	RCOR1	chr6:46097372-46098082	GM12878	blood:	n/a	n/a
3	REST	chr6:46097274-46098417	H1-neurons	neurons:	n/a	chr6:46097783-46097796
4	E2F6	chr6:46097364-46098363	H1-hESC	embryonic stem cell:	n/a	chr6:46097917-46097927 chr6:46097795-46097804 chr6:46097780-46097790
5	SP1	chr6:46097320-46097877	H1-hESC	embryonic stem cell:	n/a	chr6:46097593-46097614
6	POLR2A	chr6:46097367-46098153	MCF-7	breast:	n/a	n/a
7	POLR2A	chr6:46097060-46098735	GM12878	blood:	n/a	n/a
8	EBF1	chr6:46097264-46098102	GM12878	blood:	n/a	chr6:46098056-46098065 chr6:46098054-46098065
9	POLR2A	chr6:46097292-46098112	ECC-1	luminal epithelium:	n/a	n/a
10	MXI1	chr6:46097068-46098001	GM12878	blood:	n/a	n/a
11	RELA	chr6:46097147-46098164	GM18951	blood:	n/a	n/a
12	TBP	chr6:46097345-46097884	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr6:46097249-46097694	H1-hESC	embryonic stem cell:	n/a	n/a
14	YY1	chr6:46097356-46097967	GM12878	blood:	n/a	n/a
15	ZEB1	chr6:46097165-46097840	GM12878	blood:	n/a	n/a
16	RUNX3	chr6:46097266-46098075	GM12878	blood:	n/a	n/a
17	SP1	chr6:46097369-46097921	GM12878	blood:	n/a	chr6:46097593-46097614
18	POLR2A	chr6:46097195-46098177	Raji	blood:	n/a	n/a
19	ELF1	chr6:46097387-46098080	GM12878	blood:	n/a	n/a
20	TAF1	chr6:46097234-46098018	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr6:46097147-46098292	GM12878	blood:	n/a	n/a
22	POLR2A	chr6:46097329-46098071	GM12891	blood:	n/a	n/a
23	POLR2A	chr6:46097121-46098208	GM19099	blood:	n/a	n/a
24	SP1	chr6:46097347-46097819	GM12878	blood:	n/a	chr6:46097593-46097614
25	NFYB	chr6:46097089-46097967	GM12878	blood:	n/a	chr6:46097592-46097605 chr6:46097592-46097607 chr6:46097594-46097604 chr6:46097592-46097607 chr6:46097592-46097606
26	POLR2A	chr6:46097271-46098074	HCT-116	colon:	n/a	n/a
27	POLR2A	chr6:46097293-46098209	GM15510	blood:	n/a	n/a
28	GATA3	chr6:46097316-46097972	T-47D	breast:	n/a	chr6:46097748-46097756
29	TCF12	chr6:46097185-46098188	ECC-1	luminal epithelium:	n/a	n/a
30	SP1	chr6:46097360-46097961	H1-hESC	embryonic stem cell:	n/a	chr6:46097593-46097614
31	POLR2A	chr6:46096963-46098734	PBDE	blood:	n/a	n/a
32	POLR2A	chr6:46097268-46098252	GM19193	blood:	n/a	n/a
33	POLR2A	chr6:46097328-46098189	GM12878	blood:	n/a	n/a
34	CHD2	chr6:46097346-46098106	GM12878	blood:	n/a	chr6:46097936-46097946
35	NFYA	chr6:46097377-46097839	GM12878	blood:	n/a	chr6:46097592-46097605 chr6:46097592-46097607 chr6:46097594-46097604 chr6:46097592-46097607 chr6:46097592-46097606
36	EBF1	chr6:46097354-46098616	GM12878	blood:	n/a	chr6:46098056-46098065 chr6:46098054-46098065
37	POLR2A	chr6:46097310-46097985	HCT-116	colon:	n/a	n/a
38	TAF1	chr6:46097365-46098255	ECC-1	luminal epithelium:	n/a	n/a
39	MAZ	chr6:46097179-46098293	GM12878	blood:	n/a	n/a
40	RUNX3	chr6:46097291-46098202	GM12878	blood:	n/a	n/a
41	CTBP2	chr6:46097260-46098229	H1-hESC	embryonic stem cell:	n/a	n/a
42	KAP1	chr6:46097105-46098021	HEK293	kidney:	n/a	n/a
43	WRNIP1	chr6:46097227-46097820	GM12878	blood:	n/a	n/a
44	POLR2A	chr6:46096074-46098778	GM12891	blood:	n/a	n/a
45	SP1	chr6:46097326-46097986	HCT-116	colon:	n/a	chr6:46097593-46097614
46	SREBP2	chr6:46096067-46098783	GM12878	blood:	n/a	n/a
47	POLR2A	chr6:46097284-46098060	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr6:46097279-46097605	GM12878	blood:	n/a	n/a
49	MAX	chr6:46097202-46098378	ECC-1	luminal epithelium:	n/a	n/a
50	POLR2A	chr6:46097311-46098232	GM18951	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:46097392-46097442	H1-hESC	embryonic stem cell:	embryo
2	chr6:46097392-46097442	SK-N-MC	brain:	n/a
3	chr6:46097392-46097442	T-47D	breast:	n/a
4	chr6:46097392-46097442	GM12878	blood:	n/a
5	chr6:46097392-46097442	SKMC	muscle:	n/a
6	chr6:46097392-46097442	HepG2	liver:	n/a
7	chr6:46097392-46097442	HCM	heart:	n/a
8	chr6:46097392-46097442	HUVEC	blood vessel:	n/a
9	chr6:46097392-46097442	HNPCEpiC	eye:	n/a
10	chr6:46097392-46097442	ECC-1	luminal epithelium:	n/a
11	chr6:46097392-46097442	GM19239	blood:	n/a
12	chr6:46097392-46097442	AG10803	skin:	n/a
13	chr6:46097392-46097442	PANC-1	pancreas:	n/a
14	chr6:46097392-46097442	ProgFib	skin:	n/a
15	chr6:46097392-46097442	MCF10A-Er-Src	breast:	n/a
16	chr6:46097392-46097442	MCF-7	breast:	n/a
17	chr6:46097392-46097442	GM06990	blood:	n/a
18	chr6:46097392-46097442	HRE	kidney:	n/a
19	chr6:46097392-46097442	NH-A	brain:	n/a
20	chr6:46097392-46097442	RPTEC	kidney:	n/a
21	chr6:46097392-46097442	PFSK-1	brain:	n/a
22	chr6:46097392-46097442	A549	lung:	n/a
23	chr6:46097392-46097442	HPAEpiC	pulmonary alveolar:	n/a
24	chr6:46097392-46097442	HMEC	breast:	n/a
25	chr6:46097392-46097442	AoSMC	blood vessel:	n/a
26	chr6:46097392-46097442	HAEpiC	amniotic membrane:	n/a
27	chr6:46097392-46097442	PrEC	prostate:	n/a
28	chr6:46097392-46097442	ovcar-3	ovarian:	n/a
29	chr6:46097392-46097442	SAEC	small airway:	n/a
30	chr6:46097392-46097442	Caco-2	colon:	n/a
31	chr6:46097392-46097442	Hepatocyte	liver:	n/a
32	chr6:46097392-46097442	GM12892	blood:	n/a
33	chr6:46097392-46097442	IMR90	lung:	fetal
34	chr6:46097392-46097442	AG09309	skin:	n/a
35	chr6:46097392-46097442	K562	blood:	n/a
36	chr6:46097392-46097442	NHDF-neo	bronchial:	n/a
37	chr6:46097392-46097442	AG04449	skin:	fetal
38	chr6:46097392-46097442	U87	brain:	n/a
39	chr6:46097392-46097442	HEEpiC	esophagus:	n/a
40	chr6:46097392-46097442	HL-60	blood:	n/a
41	chr6:46097392-46097442	CMK	blood:	n/a
42	chr6:46097392-46097442	BE2_C	brain:	n/a
43	chr6:46097392-46097442	SK-N-SH_RA	brain:	n/a
44	chr6:46097392-46097442	NB4	blood:	n/a
45	chr6:46097392-46097442	AG09319	gingival:	n/a
46	chr6:46097392-46097442	SK-N-SH	brain:	n/a
47	chr6:46097392-46097442	AG04450	lung:	fetal
48	chr6:46097392-46097442	NT2-D1	testis:	n/a
49	chr6:46097392-46097442	HRCEpiC	kidney:	n/a
50	chr6:46097392-46097442	HCF	heart:	n/a

No data

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLIC5-1	chr6:46097327-46097443	ENSG00000231769.1
2	lnc-CLIC5-1	chr6:46097241-46097571	NONHSAT113004
3	lnc-CLIC5-1	chr6:46097327-46097443	ENSG00000231769.2

No data

Variant related genes	Relation type
ENPP4	TF binding region
ENSG00000231769	TF binding region
ENPP4	CpG island
ENSG00000231769	CpG island

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

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs59311337	1.00[AMR][1000 genomes]
rs9463179	0.92[AFR][1000 genomes]
rs9463192	1.00[AMR][1000 genomes]
rs9463194	1.00[AMR][1000 genomes]
rs9472729	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	nsv1022912	chr6:46093409-46116449	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:46096200-46097600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr6:46096200-46098000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
3	chr6:46096200-46098600	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr6:46096400-46098200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr6:46096400-46098200	Active TSS	Rectal Smooth Muscle	rectum
6	chr6:46096600-46097600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr6:46096600-46098200	Active TSS	Primary T cells fromperipheralblood	blood
8	chr6:46096600-46098800	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr6:46096600-46098800	Active TSS	Left Ventricle	heart
10	chr6:46096600-46098800	Active TSS	Psoas Muscle	Psoas
11	chr6:46096600-46098800	Active TSS	Right Atrium	heart
12	chr6:46096600-46098800	Active TSS	Right Ventricle	heart
13	chr6:46096800-46097600	Flanking Active TSS	Liver	Liver
14	chr6:46096800-46098000	Active TSS	H1 Cell Line	embryonic stem cell
15	chr6:46096800-46098200	Active TSS	Thymus	Thymus
16	chr6:46096800-46098200	Active TSS	GM12878-XiMat	blood
17	chr6:46096800-46098400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
18	chr6:46096800-46098400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:46096800-46098400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
20	chr6:46096800-46098400	Active TSS	Brain Anterior Caudate	brain
21	chr6:46096800-46098400	Active TSS	Duodenum Mucosa	Duodenum
22	chr6:46096800-46098400	Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr6:46096800-46098600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
24	chr6:46096800-46098600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
25	chr6:46096800-46098600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:46096800-46098800	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr6:46097000-46097600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr6:46097000-46097600	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:46097000-46097600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
30	chr6:46097000-46097600	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr6:46097000-46097600	Flanking Bivalent TSS/Enh	Fetal Lung	lung
32	chr6:46097000-46097600	Flanking Active TSS	HUVEC	blood vessel
33	chr6:46097000-46097600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr6:46097000-46098000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr6:46097000-46098200	Bivalent/Poised TSS	A549	lung
36	chr6:46097000-46098400	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:46097000-46098400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr6:46097000-46098400	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr6:46097000-46098400	Active TSS	Brain Angular Gyrus	brain
40	chr6:46097000-46098400	Active TSS	Brain Substantia Nigra	brain
41	chr6:46097000-46098400	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr6:46097000-46098400	Active TSS	Fetal Intestine Small	intestine
43	chr6:46097000-46098400	Active TSS	Stomach Smooth Muscle	stomach
44	chr6:46097000-46098600	Active TSS	H9 Cell Line	embryonic stem cell
45	chr6:46097000-46098600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
46	chr6:46097000-46098600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
47	chr6:46097000-46098600	Active TSS	Colonic Mucosa	Colon
48	chr6:46097000-46098600	Active TSS	Fetal Brain Female	brain
49	chr6:46097000-46098600	Active TSS	Gastric	stomach
50	chr6:46097000-46098800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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