Variant report

Variant	rs2856291
Chromosome Location	chr12:58138516-58138517
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:58137594-58141397	MCF10A-Er-Src	breast:	n/a	n/a
2	GABPA	chr12:58138048-58139625	SK-N-SH	brain:	n/a	n/a
3	ZNF384	chr12:58138243-58139573	K562	blood:	n/a	n/a
4	RCOR1	chr12:58137549-58139911	IMR90	lung:	n/a	n/a
5	POLR2A	chr12:58138018-58141554	U87	brain:	n/a	n/a
6	POLR2A	chr12:58138353-58140751	PANC-1	pancreas:	n/a	n/a
7	MAZ	chr12:58137824-58139357	GM12878	blood:	n/a	chr12:58139191-58139201
8	ATF2	chr12:58138004-58139627	H1-hESC	embryonic stem cell:	n/a	chr12:58138716-58138730
9	FOS	chr12:58138197-58138886	MCF10A-Er-Src	breast:	n/a	chr12:58138719-58138728
10	IRF1	chr12:58138294-58139048	K562	blood:	n/a	n/a
11	STAT1	chr12:58138091-58138527	GM12878	blood:	n/a	chr12:58138198-58138205 chr12:58138437-58138449 chr12:58138429-58138441
12	GABPA	chr12:58138266-58139705	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr12:58138231-58140454	HUVEC	blood vessel:	n/a	n/a
14	SIN3AK20	chr12:58138221-58139779	MCF-7	breast:	n/a	n/a
15	RCOR1	chr12:58138146-58139374	Hela-S3	cervix:	n/a	n/a
16	SIN3A	chr12:58138243-58139534	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr12:58137470-58141468	A549	lung:	n/a	n/a
18	RCOR1	chr12:58138222-58139399	GM12878	blood:	n/a	n/a
19	EP300	chr12:58138210-58139168	K562	blood:	n/a	chr12:58139065-58139072 chr12:58138720-58138728 chr12:58139115-58139122
20	POLR2A	chr12:58138094-58140899	GM12891	blood:	n/a	n/a
21	TAF1	chr12:58138128-58139295	SK-N-SH	brain:	n/a	n/a
22	SIX5	chr12:58138466-58138895	A549	lung:	n/a	n/a
23	NR2F2	chr12:58138484-58139116	K562	blood:	n/a	n/a
24	TBP	chr12:58138268-58139364	H1-hESC	embryonic stem cell:	n/a	n/a
25	FOXM1	chr12:58138035-58139268	GM12878	blood:	n/a	n/a
26	PBX3	chr12:58138117-58139864	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr12:58138164-58140606	NB4	blood:	n/a	n/a
28	ARID3A	chr12:58138132-58139380	HepG2	liver:	n/a	n/a
29	MAX	chr12:58138250-58139246	K562	blood:	n/a	chr12:58139191-58139201
30	POLR2A	chr12:58138445-58139808	HepG2	liver:	n/a	n/a
31	MAX	chr12:58138434-58139207	ECC-1	luminal epithelium:	n/a	chr12:58139191-58139201
32	POLR2A	chr12:58138172-58140310	Raji	blood:	n/a	n/a
33	JUN	chr12:58138210-58139025	K562	blood:	n/a	chr12:58138715-58138728 chr12:58138719-58138728
34	JUN	chr12:58137911-58139853	K562	blood:	n/a	chr12:58138715-58138728 chr12:58138719-58138728
35	POLR2A	chr12:58138326-58141516	HepG2	liver:	n/a	n/a
36	KAP1	chr12:58137675-58139388	U2OS	brain:	n/a	n/a
37	HDAC2	chr12:58138209-58138537	HepG2	liver:	n/a	n/a
38	MAZ	chr12:58138225-58139679	Hela-S3	cervix:	n/a	chr12:58139191-58139201
39	CEBPB	chr12:58138053-58139042	MCF-7	breast:	n/a	chr12:58138378-58138389
40	POLR2A	chr12:58138078-58140660	HUVEC	blood vessel:	n/a	n/a
41	FOS	chr12:58138385-58138958	K562	blood:	n/a	chr12:58138719-58138728
42	REST	chr12:58137858-58139630	H1-neurons	neurons:	n/a	n/a
43	RELA	chr12:58138211-58139502	GM15510	blood:	n/a	n/a
44	NFATC1	chr12:58138142-58140471	GM12878	blood:	n/a	n/a
45	CREB1	chr12:58137865-58140264	GM12878	blood:	n/a	chr12:58138717-58138730
46	POLR2A	chr12:58138319-58140617	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr12:58138349-58141097	U87	brain:	n/a	n/a
48	SRF	chr12:58138505-58139249	ECC-1	luminal epithelium:	n/a	n/a
49	MAZ	chr12:58138246-58140431	K562	blood:	n/a	chr12:58139191-58139201
50	EP300	chr12:58138226-58139284	GM12878	blood:	n/a	chr12:58139065-58139072 chr12:58139163-58139170 chr12:58139264-58139278 chr12:58138720-58138728 chr12:58139115-58139122

No.	Distal block	Cell Line	Cell type
1	chr12:57999349..58001291-chr12:58136626..58138684,2	MCF-7	breast:
2	chr12:57912759..57917021-chr12:58137187..58141030,5	MCF-7	breast:
3	chr12:57929794..57931809-chr12:58137772..58140062,2	MCF-7	breast:
4	chr12:57914556..57917935-chr12:58138142..58139921,3	K562	blood:
5	chr12:57985035..57986943-chr12:58137813..58139906,2	K562	blood:
6	chr12:57984385..57986376-chr12:58138351..58140314,2	K562	blood:
7	chr12:58137583..58140333-chr12:58207188..58209651,2	K562	blood:
8	chr12:57912826..57917389-chr12:58135038..58139778,7	K562	blood:
9	chr12:57943211..57945354-chr12:58136144..58138825,2	K562	blood:
10	chr12:58110256..58111795-chr12:58136834..58138576,2	K562	blood:
11	chr12:58086381..58087931-chr12:58138408..58140168,2	K562	blood:
12	chr12:58087963..58090015-chr12:58135422..58139186,3	K562	blood:
13	chr12:57914544..57916510-chr12:58137621..58139842,2	MCF-7	breast:
14	chr12:58136663..58139289-chr12:58209484..58211140,2	MCF-7	breast:
15	chr12:57480720..57482842-chr12:58137848..58140572,2	MCF-7	breast:
16	chr12:57912095..57914310-chr12:58137199..58139977,2	MCF-7	breast:

Variant related genes	Relation type
TSPAN31	TF binding region
AGAP2	TF binding region
ENSG00000175203	Chromatin interaction
ENSG00000155980	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000135407	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000166886	Chromatin interaction
ENSG00000178498	Chromatin interaction
ENSG00000135506	Chromatin interaction
ENSG00000166908	Chromatin interaction
ENSG00000269903	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv559045	chr12:58112189-58165085	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer 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	58 gene(s)	inside rSNPs	diseases
5	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	nsv899123	chr12:58118248-58155023	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv826384	chr12:58124758-58157850	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers 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	39 gene(s)	inside rSNPs	diseases
8	nsv510601	chr12:58130298-58191925	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
9	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
10	nsv826386	chr12:58135303-58150535	Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Weak transcription	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv973963	chr12:58138245-58145482	Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	22 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	chr12:58132200-58138800	Weak transcription	Gastric	stomach
2	chr12:58137800-58139400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:58137800-58139400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr12:58137800-58139400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:58137800-58140000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:58138000-58138600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr12:58138000-58138600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:58138000-58138600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr12:58138000-58138600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:58138000-58138600	Flanking Active TSS	Fetal Muscle Leg	muscle
11	chr12:58138000-58138600	Flanking Active TSS	Fetal Thymus	thymus
12	chr12:58138000-58138600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
13	chr12:58138000-58138600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr12:58138000-58138800	Enhancers	Spleen	Spleen
15	chr12:58138000-58139200	Active TSS	Esophagus	oesophagus
16	chr12:58138000-58139200	Active TSS	Rectal Smooth Muscle	rectum
17	chr12:58138000-58139400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:58138000-58139400	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr12:58138000-58139400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:58138000-58139400	Active TSS	Brain Hippocampus Middle	brain
21	chr12:58138000-58139400	Active TSS	Colon Smooth Muscle	Colon
22	chr12:58138000-58139400	Active TSS	Left Ventricle	heart
23	chr12:58138000-58139600	Active TSS	Ovary	ovary
24	chr12:58138000-58139600	Flanking Active TSS	Thymus	Thymus
25	chr12:58138000-58139600	Active TSS	HSMMtube	muscle
26	chr12:58138000-58139600	Active TSS	NHLF	lung
27	chr12:58138000-58139800	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr12:58138000-58139800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr12:58138000-58139800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr12:58138000-58140000	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr12:58138000-58140000	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr12:58138000-58140000	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr12:58138200-58138600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr12:58138200-58138600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr12:58138200-58138600	Flanking Active TSS	Fetal Brain Male	brain
36	chr12:58138200-58138600	Flanking Active TSS	Placenta	Placenta
37	chr12:58138200-58138600	Flanking Active TSS	Placenta Amnion	Placenta Amnion
38	chr12:58138200-58138800	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:58138200-58138800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:58138200-58139200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:58138200-58139200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:58138200-58139200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:58138200-58139200	Active TSS	Brain Anterior Caudate	brain
44	chr12:58138200-58139200	Active TSS	Brain Germinal Matrix	brain
45	chr12:58138200-58139200	Active TSS	Lung	lung
46	chr12:58138200-58139200	Active TSS	Stomach Smooth Muscle	stomach
47	chr12:58138200-58139400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:58138200-58139400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:58138200-58139400	Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr12:58138200-58139400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links