Variant report

Variant	rs9468346
Chromosome Location	chr6:28317714-28317715
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:392)
CpG islands
(count:122)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:392 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:28317482-28317964	U87	brain:	n/a	n/a
2	NFIC	chr6:28317179-28317894	GM12878	blood:	n/a	n/a
3	NFIC	chr6:28317490-28318437	HepG2	liver:	n/a	n/a
4	TBP	chr6:28317619-28317862	K562	blood:	n/a	n/a
5	POU2F2	chr6:28317536-28318199	GM12891	blood:	n/a	n/a
6	ELF1	chr6:28317530-28317960	SK-N-SH	brain:	n/a	chr6:28317684-28317693 chr6:28317683-28317694
7	WRNIP1	chr6:28317578-28318156	GM12878	blood:	n/a	n/a
8	NFATC1	chr6:28317434-28317945	GM12878	blood:	n/a	n/a
9	ZMIZ1	chr6:28317554-28318484	K562	blood:	n/a	n/a
10	YY1	chr6:28317594-28318182	ECC-1	luminal epithelium:	n/a	n/a
11	YY1	chr6:28317223-28317914	SK-N-SH_RA	brain:	n/a	n/a
12	MXI1	chr6:28317516-28318212	HepG2	liver:	n/a	n/a
13	POU2F2	chr6:28317581-28317881	GM12878	blood:	n/a	n/a
14	FOXM1	chr6:28317498-28317914	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:28317494-28318244	HepG2	liver:	n/a	n/a
16	SIN3A	chr6:28317468-28318151	H1-hESC	embryonic stem cell:	n/a	chr6:28317978-28317989
17	TRIM28	chr6:28317346-28318356	K562	blood:	n/a	n/a
18	NFIC	chr6:28317495-28318455	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr6:28317530-28318081	MCF-7	breast:	n/a	n/a
20	TBP	chr6:28317589-28317864	GM12878	blood:	n/a	n/a
21	TAF1	chr6:28317279-28318268	H1-neurons	neurons:	n/a	n/a
22	FOS	chr6:28317578-28317779	MCF10A-Er-Src	breast:	n/a	n/a
23	RAD21	chr6:28317568-28317830	K562	blood:	n/a	n/a
24	POLR2A	chr6:28317303-28318277	H1-neurons	neurons:	n/a	n/a
25	MAX	chr6:28317591-28317811	HepG2	liver:	n/a	n/a
26	ELF1	chr6:28317265-28318265	HCT-116	colon:	n/a	chr6:28317684-28317693 chr6:28317683-28317694
27	MAFK	chr6:28317485-28317828	HepG2	liver:	n/a	n/a
28	ELF1	chr6:28317490-28318019	K562	blood:	n/a	chr6:28317684-28317693 chr6:28317683-28317694
29	MTA3	chr6:28317626-28318180	GM12878	blood:	n/a	n/a
30	GTF2F1	chr6:28317705-28318009	H1-hESC	embryonic stem cell:	n/a	n/a
31	REST	chr6:28317491-28317963	HepG2	liver:	n/a	n/a
32	ELK4	chr6:28317546-28317855	HEK293	kidney:	n/a	chr6:28317684-28317695
33	TBL1XR1	chr6:28317264-28318493	K562	blood:	n/a	n/a
34	TAF1	chr6:28317553-28317892	GM12891	blood:	n/a	n/a
35	MAFK	chr6:28317485-28318512	K562	blood:	n/a	n/a
36	HEY1	chr6:28317497-28317952	HepG2	liver:	n/a	n/a
37	GABPA	chr6:28317340-28318157	MCF-7	breast:	n/a	n/a
38	GABPA	chr6:28317577-28317891	Hela-S3	cervix:	n/a	n/a
39	TAF1	chr6:28317437-28318258	K562	blood:	n/a	n/a
40	YY1	chr6:28317499-28318180	GM12878	blood:	n/a	n/a
41	CHD2	chr6:28317447-28317979	GM12878	blood:	n/a	n/a
42	POLR2A	chr6:28317315-28318037	GM12878	blood:	n/a	n/a
43	POLR2A	chr6:28317498-28318274	K562	blood:	n/a	n/a
44	TAF1	chr6:28317610-28317925	GM12892	blood:	n/a	n/a
45	E2F4	chr6:28317547-28317857	MCF10A-Er-Src	breast:	n/a	n/a
46	POLR2A	chr6:28317554-28318098	H1-hESC	embryonic stem cell:	n/a	n/a
47	YY1	chr6:28317521-28318070	GM12892	blood:	n/a	n/a
48	KAP1	chr6:28317527-28317974	U2OS	brain:	n/a	n/a
49	SIN3AK20	chr6:28317581-28318378	PANC-1	pancreas:	n/a	n/a
50	POLR2A	chr6:28317498-28318188	GM19099	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:28317687-28317737	MCF10A-Er-Src	breast:	n/a
2	chr6:28317687-28317737	HIPEpiC	eye:	n/a
3	chr6:28317687-28317737	Caco-2	colon:	n/a
4	chr6:28317687-28317737	HUVEC	blood vessel:	n/a
5	chr6:28317714-28317764	MCF10A-Er-Src	breast:	n/a
6	chr6:28317714-28317764	NHBE	bronchial:	n/a
7	chr6:28317687-28317737	IMR90	lung:	fetal
8	chr6:28317714-28317764	AG09309	skin:	n/a
9	chr6:28317687-28317737	HPAEpiC	pulmonary alveolar:	n/a
10	chr6:28317687-28317737	NH-A	brain:	n/a
11	chr6:28317687-28317737	NHDF-neo	bronchial:	n/a
12	chr6:28317714-28317764	ProgFib	skin:	n/a
13	chr6:28317687-28317737	HCPEpiC	choroid plexus:	n/a
14	chr6:28317687-28317737	HRPEpiC	eye:	n/a
15	chr6:28317687-28317737	Hepatocyte	liver:	n/a
16	chr6:28317687-28317737	AG10803	skin:	n/a
17	chr6:28317714-28317764	HRPEpiC	eye:	n/a
18	chr6:28317687-28317737	ovcar-3	ovarian:	n/a
19	chr6:28317714-28317764	HEK293	kidney:	embryo
20	chr6:28317714-28317764	HPAEpiC	pulmonary alveolar:	n/a
21	chr6:28317714-28317764	Jurkat	blood:	n/a
22	chr6:28317687-28317737	AG04450	lung:	fetal
23	chr6:28317687-28317737	T-47D	breast:	n/a
24	chr6:28317687-28317737	SK-N-SH_RA	brain:	n/a
25	chr6:28317714-28317764	IMR90	lung:	fetal
26	chr6:28317714-28317764	SK-N-SH_RA	brain:	n/a
27	chr6:28317687-28317737	MCF-7	breast:	n/a
28	chr6:28317714-28317764	AG09319	gingival:	n/a
29	chr6:28317687-28317737	K562	blood:	n/a
30	chr6:28317714-28317764	HCM	heart:	n/a
31	chr6:28317714-28317764	ovcar-3	ovarian:	n/a
32	chr6:28317687-28317737	NB4	blood:	n/a
33	chr6:28317687-28317737	Jurkat	blood:	n/a
34	chr6:28317687-28317737	HepG2	liver:	n/a
35	chr6:28317714-28317764	T-47D	breast:	n/a
36	chr6:28317714-28317764	HNPCEpiC	eye:	n/a
37	chr6:28317714-28317764	AG04450	lung:	fetal
38	chr6:28317714-28317764	GM06990	blood:	n/a
39	chr6:28317714-28317764	SK-N-MC	brain:	n/a
40	chr6:28317714-28317764	HMEC	breast:	n/a
41	chr6:28317687-28317737	SK-N-MC	brain:	n/a
42	chr6:28317714-28317764	SKMC	muscle:	n/a
43	chr6:28317687-28317737	RPTEC	kidney:	n/a
44	chr6:28317714-28317764	HepG2	liver:	n/a
45	chr6:28317687-28317737	SAEC	small airway:	n/a
46	chr6:28317714-28317764	A549	lung:	n/a
47	chr6:28317714-28317764	CMK	blood:	n/a
48	chr6:28317714-28317764	PrEC	prostate:	n/a
49	chr6:28317714-28317764	HCT-116	colon:	n/a
50	chr6:28317714-28317764	BJ	skin:	n/a

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28249255..28252885-chr6:28315781..28319284,4	K562	blood:
2	chr6:28109689..28111250-chr6:28315546..28317991,2	K562	blood:
3	chr6:28103114..28106211-chr6:28315199..28319125,3	K562	blood:
4	chr6:28314766..28319001-chr6:28320941..28324187,4	MCF-7	breast:
5	chr6:28183629..28195178-chr6:28316250..28325659,29	K562	blood:
6	chr6:28127970..28130555-chr6:28316475..28318965,2	K562	blood:
7	chr6:27859494..27863644-chr6:28315287..28317995,4	K562	blood:
8	chr6:27859494..27861769-chr6:28315287..28317995,2	K562	blood:
9	chr6:28300850..28305636-chr6:28315212..28320749,12	MCF-7	breast:
10	chr6:28182735..28195387-chr6:28315960..28325841,32	K562	blood:
11	chr6:28218194..28221046-chr6:28316270..28319035,4	K562	blood:
12	chr6:28219546..28223731-chr6:28316147..28319107,5	K562	blood:
13	chr6:28101857..28106060-chr6:28315199..28321034,6	K562	blood:
14	chr6:28315597..28319153-chr6:28366055..28369015,3	K562	blood:
15	chr6:28233021..28237962-chr6:28316234..28324041,9	K562	blood:

No data

Variant related genes	Relation type
ZKSCAN3	TF binding region
ZKSCAN3	CpG island
ENSG00000196331	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000226314	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000158691	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000197153	Chromatin interaction

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

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

rs_ID	r²[population]
rs17720293	1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2394098	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs34302671	1.00[ASN][1000 genomes]
rs41269283	0.90[ASN][1000 genomes]
rs9468345	0.82[YRI][hapmap]

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	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 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	chr6:28317000-28318000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr6:28317000-28318000	Active TSS	Primary hematopoietic stem cells	blood
3	chr6:28317000-28318200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:28317000-28318200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:28317000-28318200	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr6:28317000-28318200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:28317000-28318200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:28317000-28318200	Active TSS	Brain Germinal Matrix	brain
9	chr6:28317000-28318200	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr6:28317000-28318200	Active TSS	Fetal Lung	lung
11	chr6:28317000-28318200	Active TSS	HMEC	breast
12	chr6:28317000-28318200	Active TSS	NHEK	skin
13	chr6:28317000-28318400	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr6:28317000-28318400	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr6:28317000-28318400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:28317000-28318400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:28317000-28318800	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr6:28317000-28319000	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr6:28317000-28319000	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr6:28317200-28317800	Active TSS	Primary T cells fromperipheralblood	blood
21	chr6:28317200-28317800	Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr6:28317200-28318000	Active TSS	Primary B cells from peripheral blood	blood
23	chr6:28317200-28318000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:28317200-28318000	Active TSS	Brain Angular Gyrus	brain
25	chr6:28317200-28318000	Active TSS	Duodenum Mucosa	Duodenum
26	chr6:28317200-28318000	Active TSS	Fetal Thymus	thymus
27	chr6:28317200-28318200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:28317200-28318200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
29	chr6:28317200-28318200	Active TSS	Muscle Satellite Cultured Cells	--
30	chr6:28317200-28318200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:28317200-28318200	Active TSS	Brain Hippocampus Middle	brain
32	chr6:28317200-28318200	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr6:28317200-28318200	Active TSS	Brain Substantia Nigra	brain
34	chr6:28317200-28318200	Active TSS	Colon Smooth Muscle	Colon
35	chr6:28317200-28318200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr6:28317200-28318200	Active TSS	Fetal Brain Male	brain
37	chr6:28317200-28318200	Active TSS	Fetal Muscle Leg	muscle
38	chr6:28317200-28318200	Active TSS	Psoas Muscle	Psoas
39	chr6:28317200-28318200	Active TSS	Right Ventricle	heart
40	chr6:28317200-28318200	Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr6:28317200-28318200	Active TSS	Thymus	Thymus
42	chr6:28317200-28318200	Active TSS	Hela-S3	cervix
43	chr6:28317200-28318400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr6:28317200-28318400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:28317200-28318400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr6:28317200-28318400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:28317200-28318400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr6:28317200-28318400	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr6:28317200-28318400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr6:28317200-28318400	Active TSS	Aorta	Aorta

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