Variant report

Variant	rs62400353
Chromosome Location	chr6:45387899-45387900
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:45387722-45387991	ProgFib	skin:	n/a	n/a
2	RAD21	chr6:45387192-45387931	H1-hESC	embryonic stem cell:	n/a	chr6:45387625-45387637
3	CTBP2	chr6:45387213-45388179	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr6:45387212-45387937	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr6:45387224-45388229	MCF-7	breast:	n/a	n/a
6	POLR2A	chr6:45387095-45388290	HL-60	blood:	n/a	n/a
7	POLR2A	chr6:45387740-45388053	U87	brain:	n/a	n/a
8	HMGN3	chr6:45387328-45388125	K562	blood:	n/a	n/a
9	POLR2A	chr6:45387883-45388906	H1-neurons	neurons:	n/a	n/a
10	BACH1	chr6:45387208-45388133	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:45387854-45387904	PrEC	prostate:	n/a
2	chr6:45387854-45387904	HUVEC	blood vessel:	n/a
3	chr6:45387854-45387904	PANC-1	pancreas:	n/a
4	chr6:45387854-45387904	GM19239	blood:	n/a
5	chr6:45387854-45387904	U87	brain:	n/a
6	chr6:45387854-45387904	HL-60	blood:	n/a
7	chr6:45387854-45387904	HMEC	breast:	n/a
8	chr6:45387854-45387904	AG04450	lung:	fetal
9	chr6:45387854-45387904	CMK	blood:	n/a
10	chr6:45387854-45387904	SAEC	small airway:	n/a
11	chr6:45387854-45387904	HCT-116	colon:	n/a
12	chr6:45387854-45387904	HCM	heart:	n/a
13	chr6:45387854-45387904	HAEpiC	amniotic membrane:	n/a
14	chr6:45387854-45387904	RPTEC	kidney:	n/a
15	chr6:45387854-45387904	HCF	heart:	n/a
16	chr6:45387854-45387904	MCF-7	breast:	n/a
17	chr6:45387854-45387904	HRCEpiC	kidney:	n/a
18	chr6:45387854-45387904	GM12878	blood:	n/a
19	chr6:45387854-45387904	HIPEpiC	eye:	n/a
20	chr6:45387854-45387904	SK-N-SH_RA	brain:	n/a
21	chr6:45387854-45387904	LNCaP	prostate:	n/a
22	chr6:45387854-45387904	NHBE	bronchial:	n/a
23	chr6:45387854-45387904	AG10803	skin:	n/a
24	chr6:45387854-45387904	Caco-2	colon:	n/a
25	chr6:45387854-45387904	NH-A	brain:	n/a
26	chr6:45387854-45387904	AG09309	skin:	n/a
27	chr6:45387854-45387904	GM12892	blood:	n/a
28	chr6:45387854-45387904	ProgFib	skin:	n/a
29	chr6:45387854-45387904	NT2-D1	testis:	n/a
30	chr6:45387854-45387904	H1-hESC	embryonic stem cell:	embryo
31	chr6:45387854-45387904	K562	blood:	n/a
32	chr6:45387854-45387904	A549	lung:	n/a
33	chr6:45387854-45387904	BJ	skin:	n/a
34	chr6:45387854-45387904	HNPCEpiC	eye:	n/a
35	chr6:45387854-45387904	MCF10A-Er-Src	breast:	n/a
36	chr6:45387854-45387904	ovcar-3	ovarian:	n/a
37	chr6:45387854-45387904	Jurkat	blood:	n/a
38	chr6:45387854-45387904	HEK293	kidney:	embryo
39	chr6:45387854-45387904	PFSK-1	brain:	n/a
40	chr6:45387854-45387904	AG04449	skin:	fetal
41	chr6:45387854-45387904	IMR90	lung:	fetal
42	chr6:45387854-45387904	HEEpiC	esophagus:	n/a
43	chr6:45387854-45387904	AG09319	gingival:	n/a
44	chr6:45387854-45387904	NB4	blood:	n/a
45	chr6:45387854-45387904	NHDF-neo	bronchial:	n/a
46	chr6:45387854-45387904	ECC-1	luminal epithelium:	n/a
47	chr6:45387854-45387904	HRPEpiC	eye:	n/a
48	chr6:45387854-45387904	HPAEpiC	pulmonary alveolar:	n/a
49	chr6:45387854-45387904	GM06990	blood:	n/a
50	chr6:45387854-45387904	SKMC	muscle:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:45387629..45388223-chr6:45574849..45575456,2	MCF-7	breast:
2	chr6:45343194..45347445-chr6:45386856..45389425,4	MCF-7	breast:
3	chr6:45387795..45389727-chr6:45621998..45623537,2	MCF-7	breast:
4	chr6:45385643..45388546-chr6:45402027..45403903,2	K562	blood:
5	chr6:44621438..44623552-chr6:45385736..45388859,3	MCF-7	breast:
6	chr6:45343131..45346998-chr6:45386286..45389886,4	MCF-7	breast:

No data

Variant related genes	Relation type
RUNX2	TF binding region
RUNX2	CpG island
ENSG00000196284	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10456553	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10948233	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12192267	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197755	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201563	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12203052	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211510	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1321078	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1321079	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1321080	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17209895	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1852983	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1852984	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2064628	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2894641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72862930	0.89[AMR][1000 genomes];0.87[EUR][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	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45384800-45388000	Weak transcription	Hela-S3	cervix
2	chr6:45386800-45389400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:45386800-45389400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:45387000-45388400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr6:45387000-45388800	Flanking Active TSS	NH-A	brain
6	chr6:45387000-45389000	Flanking Active TSS	Osteobl	bone
7	chr6:45387000-45389400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
8	chr6:45387000-45389800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr6:45387000-45391800	Bivalent Enhancer	Fetal Brain Male	brain
10	chr6:45387000-45392200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr6:45387200-45388000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr6:45387200-45388000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:45387200-45388000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:45387200-45388000	Active TSS	Brain Substantia Nigra	brain
15	chr6:45387200-45388000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
16	chr6:45387200-45388200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:45387200-45388200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
18	chr6:45387200-45388200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:45387200-45388200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:45387200-45388200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
21	chr6:45387200-45388200	Flanking Bivalent TSS/Enh	Liver	Liver
22	chr6:45387200-45388200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
23	chr6:45387200-45388200	Flanking Active TSS	Ovary	ovary
24	chr6:45387200-45388200	Flanking Bivalent TSS/Enh	Sigmoid Colon	Sigmoid Colon
25	chr6:45387200-45388200	Enhancers	Spleen	Spleen
26	chr6:45387200-45388400	Bivalent Enhancer	Stomach Mucosa	stomach
27	chr6:45387200-45388600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:45387200-45388600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:45387200-45388600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
30	chr6:45387200-45388600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
31	chr6:45387200-45388800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
32	chr6:45387200-45388800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
33	chr6:45387200-45388800	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:45387200-45389000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
35	chr6:45387200-45389000	Flanking Active TSS	HMEC	breast
36	chr6:45387200-45389000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
37	chr6:45387200-45389200	Bivalent Enhancer	Brain Germinal Matrix	brain
38	chr6:45387200-45389400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:45387200-45389400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr6:45387200-45389600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
41	chr6:45387200-45389600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
42	chr6:45387200-45390800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
43	chr6:45387400-45388000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
44	chr6:45387400-45388000	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
45	chr6:45387400-45388000	Enhancers	Dnd41	blood
46	chr6:45387400-45388200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:45387400-45388200	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:45387400-45388200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr6:45387400-45388200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
50	chr6:45387400-45388200	Flanking Bivalent TSS/Enh	Left Ventricle	heart

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