Variant report

Variant	rs3802987
Chromosome Location	chr12:57917602-57917603
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:55)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:55 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57916882-57919110	U87	brain:	n/a	n/a
2	POLR2A	chr12:57915733-57918696	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr12:57916844-57917719	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr12:57917038-57917781	GM12878	blood:	n/a	n/a
5	MAZ	chr12:57917426-57917708	HepG2	liver:	n/a	n/a
6	POLR2A	chr12:57916931-57917924	U87	brain:	n/a	n/a
7	HCFC1	chr12:57915227-57917771	Hela-S3	cervix:	n/a	n/a
8	BCL3	chr12:57916903-57917779	A549	lung:	n/a	chr12:57917163-57917172
9	POLR2A	chr12:57915483-57918252	Hela-S3	cervix:	n/a	n/a
10	BCL3	chr12:57916907-57917922	A549	lung:	n/a	chr12:57917163-57917172
11	POLR2A	chr12:57916867-57917746	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr12:57916912-57917845	HCT-116	colon:	n/a	n/a
13	MTA3	chr12:57916889-57918162	GM12878	blood:	n/a	n/a
14	MAZ	chr12:57915727-57917823	GM12878	blood:	n/a	chr12:57916339-57916349 chr12:57916084-57916093 chr12:57916730-57916740
15	POLR2A	chr12:57911713-57919299	SK-N-MC	brain:	n/a	n/a
16	PML	chr12:57916912-57918215	GM12878	blood:	n/a	n/a
17	POLR2A	chr12:57916947-57917652	Hela-S3	cervix:	n/a	n/a
18	EBF1	chr12:57917238-57917850	GM12878	blood:	n/a	chr12:57917633-57917646 chr12:57917635-57917645 chr12:57917635-57917644 chr12:57917634-57917644 chr12:57917633-57917644
19	POLR2A	chr12:57915797-57918188	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr12:57917555-57918192	MCF-7	breast:	n/a	n/a
21	POLR2A	chr12:57917373-57917789	HepG2	liver:	n/a	n/a
22	TEAD4	chr12:57916833-57917616	K562	blood:	n/a	n/a
23	POLR2A	chr12:57917499-57918427	GM12878	blood:	n/a	n/a
24	POLR2A	chr12:57915689-57917735	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr12:57908382-57921207	K562	blood:	n/a	n/a
26	POLR2A	chr12:57917025-57917669	HepG2	liver:	n/a	n/a
27	REST	chr12:57916934-57917718	A549	lung:	n/a	chr12:57917607-57917617
28	RCOR1	chr12:57917524-57917604	GM12878	blood:	n/a	n/a
29	NFIC	chr12:57917168-57917734	GM12878	blood:	n/a	n/a
30	POLR2A	chr12:57915112-57917615	HL-60	blood:	n/a	n/a
31	POLR2A	chr12:57917100-57917726	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr12:57915375-57927219	K562	blood:	n/a	n/a
33	POLR2A	chr12:57912610-57921102	K562	blood:	n/a	n/a
34	MAZ	chr12:57915522-57917725	IMR90	lung:	n/a	chr12:57916339-57916349 chr12:57916084-57916093 chr12:57916730-57916740
35	STAT5A	chr12:57916978-57918255	GM12878	blood:	n/a	chr12:57917506-57917514
36	CUX1	chr12:57917594-57917607	K562	blood:	n/a	n/a
37	POLR2A	chr12:57915222-57917641	HL-60	blood:	n/a	n/a
38	SIX5	chr12:57916932-57917666	A549	lung:	n/a	n/a
39	POLR2A	chr12:57908062-57920927	K562	blood:	n/a	n/a
40	POLR2A	chr12:57917406-57917639	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr12:57916895-57917793	HepG2	liver:	n/a	n/a
42	POLR2A	chr12:57917450-57919020	K562	blood:	n/a	n/a
43	USF2	chr12:57917083-57917813	Hela-S3	cervix:	n/a	n/a
44	EP300	chr12:57915742-57917657	ECC-1	luminal epithelium:	n/a	chr12:57916652-57916661
45	PML	chr12:57916884-57917735	K562	blood:	n/a	n/a
46	ZNF263	chr12:57917064-57917901	HEK293-T-REx	kidney:	n/a	n/a
47	POLR2A	chr12:57916885-57918266	GM12878	blood:	n/a	n/a
48	POLR2A	chr12:57916870-57918716	PFSK-1	brain:	n/a	n/a
49	NR2F2	chr12:57916882-57917822	K562	blood:	n/a	n/a
50	POLR2A	chr12:57916888-57918820	U87	brain:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57879207..57888227-chr12:57906247..57918451,36	K562	blood:
2	chr12:57915482..57918597-chr12:58119014..58121092,3	MCF-7	breast:
3	chr12:57914556..57917935-chr12:58138142..58139921,3	K562	blood:
4	chr12:57916512..57918954-chr12:58138893..58140769,2	MCF-7	breast:
5	chr12:57915284..57917737-chr12:58135302..58137824,2	K562	blood:
6	chr12:57916469..57918452-chr12:58024223..58025919,2	K562	blood:
7	chr12:57082052..57084048-chr12:57915298..57917787,2	K562	blood:
8	chr12:57850154..57858218-chr12:57910899..57919538,20	K562	blood:
9	chr12:57848374..57850176-chr12:57916596..57918121,2	MCF-7	breast:
10	chr12:57916381..57918711-chr12:58131475..58134282,2	MCF-7	breast:
11	chr12:57914860..57917603-chr12:58144909..58148802,3	K562	blood:
12	chr12:57911699..57918406-chr12:58000825..58010019,18	K562	blood:
13	chr12:57889487..57901620-chr12:57907600..57919310,30	K562	blood:
14	chr12:57912818..57918945-chr12:58145879..58149998,6	MCF-7	breast:
15	chr12:57879869..57888452-chr12:57905809..57918310,36	K562	blood:
16	chr12:57881044..57886958-chr12:57910925..57918058,16	MCF-7	breast:
17	chr12:57916409..57919050-chr12:57983099..57985919,3	MCF-7	breast:

No data

Variant related genes	Relation type
MBD6	TF binding region
DDIT3	TF binding region
MIR616	TF binding region
ENSG00000240771	Chromatin interaction
ENSG00000123329	Chromatin interaction
ENSG00000166908	Chromatin interaction
ENSG00000135454	Chromatin interaction
ENSG00000139269	Chromatin interaction
ENSG00000135452	Chromatin interaction
ENSG00000139266	Chromatin interaction
ENSG00000135439	Chromatin interaction
ENSG00000111087	Chromatin interaction
ENSG00000255737	Chromatin interaction
ENSG00000110958	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000257499	Chromatin interaction
ENSG00000135446	Chromatin interaction
ENSG00000178498	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2278846	1.00[ASN][1000 genomes]
rs2290297	0.92[ASN][1000 genomes]
rs2305390	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
2	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer 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	96 gene(s)	inside rSNPs	diseases
4	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	nsv469411	chr12:57844049-57921188	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers 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	89 gene(s)	inside rSNPs	diseases
8	nsv559032	chr12:57844049-57921188	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
9	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
10	nsv899119	chr12:57851182-57923451	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
11	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
12	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
13	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers 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	126 gene(s)	inside rSNPs	diseases
14	nsv899120	chr12:57886609-57921188	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
15	esv3429239	chr12:57915210-57918058	Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	41 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57912400-57918600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr12:57916000-57917800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:57916000-57917800	Active TSS	Aorta	Aorta
4	chr12:57916200-57917800	Active TSS	Lung	lung
5	chr12:57916400-57917800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:57917000-57917800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr12:57917000-57917800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr12:57917000-57917800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr12:57917000-57917800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:57917000-57917800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr12:57917000-57917800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:57917000-57917800	Flanking Active TSS	Colonic Mucosa	Colon
13	chr12:57917000-57917800	Flanking Active TSS	Fetal Brain Male	brain
14	chr12:57917000-57917800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr12:57917000-57918000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:57917000-57918000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
17	chr12:57917000-57918000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr12:57917000-57918000	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr12:57917000-57918000	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr12:57917000-57918000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr12:57917000-57918000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:57917000-57918000	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr12:57917000-57918000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
24	chr12:57917000-57918000	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr12:57917000-57918000	Flanking Active TSS	Fetal Brain Female	brain
26	chr12:57917000-57918000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr12:57917000-57918200	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr12:57917000-57918400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr12:57917000-57919000	Transcr. at gene 5' and 3'	Dnd41	blood
30	chr12:57917200-57917800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr12:57917200-57917800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr12:57917200-57917800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr12:57917200-57917800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:57917200-57917800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr12:57917200-57917800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:57917200-57917800	Flanking Active TSS	Brain Angular Gyrus	brain
37	chr12:57917200-57917800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr12:57917200-57917800	Flanking Active TSS	Fetal Lung	lung
39	chr12:57917200-57917800	Flanking Active TSS	Pancreas	Pancrea
40	chr12:57917200-57917800	Flanking Active TSS	Thymus	Thymus
41	chr12:57917200-57917800	Flanking Active TSS	NHLF	lung
42	chr12:57917200-57917800	Flanking Active TSS	Osteobl	bone
43	chr12:57917200-57918000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
44	chr12:57917200-57918000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr12:57917200-57918000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr12:57917200-57918000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:57917200-57918000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:57917200-57918000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:57917200-57918000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:57917200-57918000	Flanking Active TSS	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links