Variant report

Variant	rs11837790
Chromosome Location	chr12:57117485-57117486
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57117479-57119648	MCF10A-Er-Src	breast:	n/a	n/a
2	MXI1	chr12:57117477-57119619	IMR90	lung:	n/a	n/a
3	POLR2A	chr12:57117432-57119689	H1-hESC	embryonic stem cell:	n/a	n/a
4	CHD1	chr12:57117473-57119574	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:57117397-57118109	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr12:57117211-57119795	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:57117110-57119791	U87	brain:	n/a	n/a
8	MXI1	chr12:57117021-57118035	K562	blood:	n/a	n/a
9	POLR2A	chr12:57117326-57119712	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr12:57117480-57119732	GM12878	blood:	n/a	n/a
11	POLR2A	chr12:57117445-57119614	U87	brain:	n/a	n/a
12	CHD1	chr12:57116778-57119555	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr12:57117290-57119785	U87	brain:	n/a	n/a
14	POLR2A	chr12:57117472-57118253	PBDE	blood:	n/a	n/a
15	POLR2A	chr12:57116545-57117501	PANC-1	pancreas:	n/a	n/a
16	IRF1	chr12:57117413-57117862	K562	blood:	n/a	n/a
17	POLR2A	chr12:57117453-57118099	Hela-S3	cervix:	n/a	n/a
18	HCFC1	chr12:57117481-57120192	Hela-S3	cervix:	n/a	n/a
19	NFATC1	chr12:57117380-57118249	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:57116665-57119772	PFSK-1	brain:	n/a	n/a
21	POLR2A	chr12:57117170-57119785	SK-N-MC	brain:	n/a	n/a
22	MXI1	chr12:57116480-57120181	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr12:57117365-57118004	HepG2	liver:	n/a	n/a
24	POLR2A	chr12:57117445-57119671	U87	brain:	n/a	n/a
25	POLR2A	chr12:57117378-57120002	GM12891	blood:	n/a	n/a
26	POLR2A	chr12:57117243-57118217	K562	blood:	n/a	n/a
27	POLR2A	chr12:57117484-57119895	K562	blood:	n/a	n/a
28	POLR2A	chr12:57117417-57119637	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57075341..57085478-chr12:57112447..57121011,58	MCF-7	breast:
2	chr12:57116864..57121762-chr12:57140480..57149366,20	K562	blood:
3	chr12:57117154..57122230-chr12:57122473..57127950,8	K562	blood:
4	chr12:57117403..57120848-chr12:57123897..57127833,5	MCF-7	breast:
5	chr1:852957..855420-chr12:57116764..57119189,2	MCF-7	breast:
6	chr12:57117159..57119489-chr12:57914533..57916753,2	K562	blood:
7	chr12:57115537..57117655-chr17:56707666..56710066,3	MCF-7	breast:
8	chr12:57116631..57120456-chr12:57479265..57482503,6	MCF-7	breast:
9	chr12:57026523..57033046-chr12:57115223..57120839,17	MCF-7	breast:
10	chr12:57035906..57041425-chr12:57115344..57122353,14	K562	blood:
11	chr12:57116832..57120019-chr12:57136517..57139167,4	K562	blood:
12	chr12:57038025..57041646-chr12:57113711..57120620,12	MCF-7	breast:
13	chr12:57074578..57085543-chr12:57108746..57121559,55	K562	blood:
14	chr12:57117372..57120851-chr12:57140459..57146973,9	MCF-7	breast:
15	chr12:57036857..57041663-chr12:57115375..57121628,17	MCF-7	breast:
16	chr12:57036938..57041843-chr12:57115310..57120529,12	K562	blood:
17	chr12:57117044..57122605-chr12:57141917..57149366,15	K562	blood:
18	chr12:57076604..57085974-chr12:57112559..57120474,46	MCF-7	breast:
19	chr12:57029325..57031901-chr12:57117186..57120147,2	K562	blood:
20	chr12:56583529..56586106-chr12:57117314..57120068,2	MCF-7	breast:
21	chr12:57078475..57085183-chr12:57112918..57121559,38	K562	blood:
22	chr12:57022951..57032187-chr12:57113330..57121462,17	K562	blood:
23	chr12:57115452..57117913-chr12:57483111..57485379,2	K562	blood:

No data

Variant related genes	Relation type
NACA	TF binding region
ENSG00000207031	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000025423	Chromatin interaction
ENSG00000223764	Chromatin interaction
ENSG00000198056	Chromatin interaction
ENSG00000110958	Chromatin interaction
ENSG00000196531	Chromatin interaction
ENSG00000110955	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000076108	Chromatin interaction
ENSG00000166881	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11171910	1.00[CEU][hapmap]
rs11833209	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11833254	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11833282	0.90[AFR][1000 genomes]
rs11837737	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11838315	0.81[AFR][1000 genomes]
rs12312913	1.00[CEU][hapmap]
rs12314491	1.00[CEU][hapmap]
rs1527140	1.00[CEU][hapmap]
rs17118865	0.90[ASW][hapmap];1.00[CEU][hapmap];0.92[YRI][hapmap]
rs17118901	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs17118921	1.00[CEU][hapmap];0.81[AFR][1000 genomes]
rs17118953	1.00[ASW][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2030909	1.00[CEU][hapmap]
rs4262757	0.83[AFR][1000 genomes]
rs55962252	0.89[AFR][1000 genomes]
rs56258039	0.81[AFR][1000 genomes]
rs60574031	0.88[AFR][1000 genomes]
rs7307578	0.90[ASW][hapmap];1.00[CEU][hapmap];0.92[YRI][hapmap]
rs7974103	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[LWK][hapmap];0.81[MKK][hapmap];0.92[YRI][hapmap]
rs7974600	1.00[CEU][hapmap];0.92[YRI][hapmap]
rs7977632	0.81[ASW][hapmap];1.00[CEU][hapmap];0.96[LWK][hapmap];0.97[MKK][hapmap];0.88[YRI][hapmap]
rs941210	1.00[CEU][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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer 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 miRNA target site	181 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	chr12:57109600-57117800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr12:57110400-57117600	Genic enhancers	Primary B cells from peripheral blood	blood
3	chr12:57113400-57117800	Transcr. at gene 5' and 3'	Hela-S3	cervix
4	chr12:57113600-57118200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
5	chr12:57113800-57118800	Transcr. at gene 5' and 3'	K562	blood
6	chr12:57114200-57117600	Enhancers	Stomach Mucosa	stomach
7	chr12:57114400-57118800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
8	chr12:57114400-57119200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:57114600-57118400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
10	chr12:57114800-57117600	Enhancers	Small Intestine	intestine
11	chr12:57114800-57117800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
12	chr12:57114800-57118000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
13	chr12:57114800-57118000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:57114800-57118800	Transcr. at gene 5' and 3'	Dnd41	blood
15	chr12:57115000-57117600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:57115000-57118000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
17	chr12:57115200-57117600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:57115200-57117600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:57115200-57118000	Transcr. at gene 5' and 3'	NH-A	brain
20	chr12:57115200-57118200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
21	chr12:57115400-57117600	Weak transcription	Esophagus	oesophagus
22	chr12:57115400-57117800	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
23	chr12:57115400-57118000	Transcr. at gene 5' and 3'	NHEK	skin
24	chr12:57115400-57118200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
25	chr12:57115400-57118600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:57115400-57118800	Transcr. at gene 5' and 3'	A549	lung
27	chr12:57115600-57117600	Weak transcription	Lung	lung
28	chr12:57115600-57118200	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
29	chr12:57115800-57117600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:57115800-57119800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:57116000-57117600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr12:57116000-57117800	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
33	chr12:57116000-57118200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:57116000-57118200	Flanking Active TSS	Rectal Smooth Muscle	rectum
35	chr12:57116000-57118600	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr12:57116200-57117600	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr12:57116200-57117800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr12:57116200-57118400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:57116200-57118600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:57116400-57117600	Enhancers	Placenta Amnion	Placenta Amnion
41	chr12:57116400-57117800	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:57116400-57118000	Flanking Active TSS	Brain Hippocampus Middle	brain
43	chr12:57116400-57118400	Transcr. at gene 5' and 3'	Osteobl	bone
44	chr12:57116600-57117600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr12:57116600-57117600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:57116600-57117600	Weak transcription	Gastric	stomach
47	chr12:57116600-57117600	Weak transcription	Spleen	Spleen
48	chr12:57116600-57117800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:57116600-57118000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr12:57116600-57118800	Active TSS	Right Atrium	heart

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