Variant report

Variant	rs12460778
Chromosome Location	chr19:55866929-55866930
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:61)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr19:55866865-55867120	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr19:55866786-55867263	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr19:55866838-55867396	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr19:55866811-55867255	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr19:55866826-55867285	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr19:55866806-55867338	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr19:55866915-55867128	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr19:55866888-55867263	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr19:55866809-55867232	MCF10A-Er-Src	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:55866907-55866957	HRE	kidney:	n/a
2	chr19:55866907-55866957	RPTEC	kidney:	n/a
3	chr19:55866907-55866957	HCM	heart:	n/a
4	chr19:55866907-55866957	PrEC	prostate:	n/a
5	chr19:55866907-55866957	T-47D	breast:	n/a
6	chr19:55866907-55866957	HEEpiC	esophagus:	n/a
7	chr19:55866907-55866957	HAEpiC	amniotic membrane:	n/a
8	chr19:55866907-55866957	Hela-S3	cervix:	n/a
9	chr19:55866907-55866957	HNPCEpiC	eye:	n/a
10	chr19:55866907-55866957	SK-N-SH	brain:	n/a
11	chr19:55866907-55866957	ECC-1	luminal epithelium:	n/a
12	chr19:55866907-55866957	HUVEC	blood vessel:	n/a
13	chr19:55866907-55866957	MCF10A-Er-Src	breast:	n/a
14	chr19:55866907-55866957	CMK	blood:	n/a
15	chr19:55866907-55866957	LNCaP	prostate:	n/a
16	chr19:55866907-55866957	SK-N-SH_RA	brain:	n/a
17	chr19:55866907-55866957	Hepatocyte	liver:	n/a
18	chr19:55866907-55866957	MCF-7	breast:	n/a
19	chr19:55866907-55866957	HMEC	breast:	n/a
20	chr19:55866907-55866957	Jurkat	blood:	n/a
21	chr19:55866907-55866957	A549	lung:	n/a
22	chr19:55866907-55866957	AG04450	lung:	fetal
23	chr19:55866907-55866957	SAEC	small airway:	n/a
24	chr19:55866907-55866957	AG04449	skin:	fetal
25	chr19:55866907-55866957	AG10803	skin:	n/a
26	chr19:55866907-55866957	NHDF-neo	bronchial:	n/a
27	chr19:55866907-55866957	HPAEpiC	pulmonary alveolar:	n/a
28	chr19:55866907-55866957	GM12878	blood:	n/a
29	chr19:55866907-55866957	BE2_C	brain:	n/a
30	chr19:55866907-55866957	GM12891	blood:	n/a
31	chr19:55866907-55866957	ProgFib	skin:	n/a
32	chr19:55866907-55866957	HL-60	blood:	n/a
33	chr19:55866907-55866957	AoSMC	blood vessel:	n/a
34	chr19:55866907-55866957	SKMC	muscle:	n/a
35	chr19:55866907-55866957	Caco-2	colon:	n/a
36	chr19:55866907-55866957	NHBE	bronchial:	n/a
37	chr19:55866907-55866957	GM06990	blood:	n/a
38	chr19:55866907-55866957	HCT-116	colon:	n/a
39	chr19:55866907-55866957	HRPEpiC	eye:	n/a
40	chr19:55866907-55866957	SK-N-MC	brain:	n/a
41	chr19:55866907-55866957	GM12892	blood:	n/a
42	chr19:55866907-55866957	HCF	heart:	n/a
43	chr19:55866907-55866957	HepG2	liver:	n/a
44	chr19:55866907-55866957	HCPEpiC	choroid plexus:	n/a
45	chr19:55866907-55866957	H1-hESC	embryonic stem cell:	embryo
46	chr19:55866907-55866957	U87	brain:	n/a
47	chr19:55866907-55866957	BJ	skin:	n/a
48	chr19:55866907-55866957	K562	blood:	n/a
49	chr19:55866907-55866957	HRCEpiC	kidney:	n/a
50	chr19:55866907-55866957	NB4	blood:	n/a

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55864929..55868342-chr19:55869494..55871064,3	MCF-7	breast:
2	chr19:55865530..55867437-chr19:55869222..55871050,2	K562	blood:
3	chr19:55725474..55728358-chr19:55864550..55866958,2	K562	blood:
4	chr19:55863699..55867009-chr19:55895864..55899065,4	MCF-7	breast:
5	chr19:55864955..55867658-chr19:55880222..55883231,3	MCF-7	breast:
6	chr19:55865626..55867203-chr19:55869204..55871320,2	K562	blood:
7	chr19:55864065..55867080-chr19:55895058..55897568,4	K562	blood:
8	chr19:55865908..55868131-chr19:55880960..55883611,2	MCF-7	breast:
9	chr19:55865213..55868465-chr19:55868824..55871801,4	MCF-7	breast:
10	chr19:55864307..55867114-chr19:56165229..56167152,3	K562	blood:
11	chr19:55866844..55868519-chr19:55877122..55879184,2	K562	blood:
12	chr19:55862642..55868480-chr19:55895176..55899926,10	K562	blood:
13	chr19:55865425..55868489-chr19:55917598..55920755,3	MCF-7	breast:
14	chr19:55853470..55856275-chr19:55866568..55868839,2	MCF-7	breast:

No data

Variant related genes	Relation type
COX6B2	TF binding region
COX6B2	CpG island
ENSG00000095752	Chromatin interaction
ENSG00000267649	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000133247	Chromatin interaction
ENSG00000267706	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000233493	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11084396	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12971931	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1816335	chr19:55683977-55901099	Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912455	chr19:55725410-55879872	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
5	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
6	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
7	nsv912460	chr19:55814881-55897327	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
8	nsv912461	chr19:55845386-55897327	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
9	nsv470162	chr19:55845386-55902257	Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
10	nsv912462	chr19:55845386-55925500	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
11	nsv912463	chr19:55845386-56004901	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
12	nsv912464	chr19:55850269-55921164	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
13	esv1799638	chr19:55850652-55883879	Weak transcription Strong transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
14	nsv516199	chr19:55854313-55901099	Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
15	nsv912465	chr19:55854313-55935184	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
16	esv3430654	chr19:55864590-55867488	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	esv3405241	chr19:55865165-55868013	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55865400-55867000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
2	chr19:55865600-55867000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
3	chr19:55865600-55867000	Bivalent Enhancer	Fetal Muscle Leg	muscle
4	chr19:55865800-55867400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:55865800-55867800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr19:55866000-55867000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
7	chr19:55866000-55867000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr19:55866000-55867200	Bivalent Enhancer	Fetal Stomach	stomach
9	chr19:55866000-55867400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr19:55866000-55867400	Enhancers	HMEC	breast
11	chr19:55866000-55867400	Enhancers	NHEK	skin
12	chr19:55866200-55867000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:55866200-55880600	Weak transcription	Right Atrium	heart
14	chr19:55866400-55867000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:55866400-55867200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
16	chr19:55866400-55867400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr19:55866400-55867600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:55866400-55867800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr19:55866600-55867000	Enhancers	K562	blood
20	chr19:55866800-55867000	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
21	chr19:55866800-55867000	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
22	chr19:55866800-55867000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
23	chr19:55866800-55867000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
24	chr19:55866800-55867000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr19:55866800-55867000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:55866800-55867000	Bivalent Enhancer	Fetal Lung	lung
27	chr19:55866800-55867000	Bivalent Enhancer	Spleen	Spleen
28	chr19:55866800-55867000	Bivalent Enhancer	NH-A	brain
29	chr19:55866800-55867200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
30	chr19:55866800-55867200	Bivalent Enhancer	HSMM	muscle
31	chr19:55866800-55867400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr19:55866800-55867400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr19:55866800-55867400	Bivalent Enhancer	Esophagus	oesophagus

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