Variant report

Variant	rs10783299
Chromosome Location	chr12:49390677-49390678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:226)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:226 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr12:49390472-49390842	A549	lung:	n/a	n/a
2	CTCF	chr12:49390640-49390790	GM12878	blood:	n/a	n/a
3	CTCF	chr12:49390620-49390770	AG10803	skin:	n/a	n/a
4	TEAD4	chr12:49390510-49390849	H1-hESC	embryonic stem cell:	n/a	n/a
5	YY1	chr12:49390569-49390878	K562	blood:	n/a	n/a
6	CTCF	chr12:49390574-49390886	A549	lung:	n/a	n/a
7	TCF7L2	chr12:49390556-49390979	PANC-1	pancreas:	n/a	n/a
8	MYC	chr12:49390601-49390821	K562	blood:	n/a	n/a
9	CTCF	chr12:49390532-49390841	HepG2	liver:	n/a	n/a
10	CTCF	chr12:49390520-49390868	SK-N-SH_RA	brain:	n/a	n/a
11	CTCF	chr12:49390640-49390790	GM12868	blood:	n/a	n/a
12	YY1	chr12:49390466-49391052	HepG2	liver:	n/a	n/a
13	CTCF	chr12:49390580-49390730	GM12870	blood:	n/a	n/a
14	CTCF	chr12:49390559-49390816	GM19239	blood:	n/a	n/a
15	CTCF	chr12:49390660-49390810	GM12865	blood:	n/a	n/a
16	CTCF	chr12:49390620-49390770	HMF	breast:	n/a	n/a
17	CTCF	chr12:49390580-49390730	HCM	heart:	n/a	n/a
18	RAD21	chr12:49390385-49390953	A549	lung:	n/a	n/a
19	GABPA	chr12:49390453-49390879	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr12:49390447-49390907	HepG2	liver:	n/a	n/a
21	CTCF	chr12:49390620-49390770	GM12864	blood:	n/a	n/a
22	RAD21	chr12:49390468-49390848	H1-hESC	embryonic stem cell:	n/a	n/a
23	SMC3	chr12:49390503-49390889	GM12878	blood:	n/a	n/a
24	CTCF	chr12:49390620-49390770	HA-sp	spinal cord:	n/a	n/a
25	CTCF	chr12:49390620-49390770	GM12872	blood:	n/a	n/a
26	RELA	chr12:49390585-49391389	GM19193	blood:	n/a	n/a
27	CTCF	chr12:49390620-49390770	AG09319	gingival:	n/a	n/a
28	CTCF	chr12:49390640-49390790	BE2_C	brain:	n/a	n/a
29	RAD21	chr12:49390520-49390920	SK-N-SH_RA	brain:	n/a	n/a
30	MAX	chr12:49390429-49391002	A549	lung:	n/a	n/a
31	CTCF	chr12:49390600-49390750	GM12801	blood:	n/a	n/a
32	CTCF	chr12:49390620-49390770	NHDF-neo	bronchial:	n/a	n/a
33	CREB1	chr12:49390506-49390895	A549	lung:	n/a	n/a
34	YY1	chr12:49390571-49391143	GM12892	blood:	n/a	n/a
35	CTCF	chr12:49390465-49390970	K562	blood:	n/a	n/a
36	CTCF	chr12:49390660-49390810	GM12871	blood:	n/a	n/a
37	CTCF	chr12:49390620-49390770	HCFaa	heart:	n/a	n/a
38	CTCF	chr12:49390580-49390730	A549	lung:	n/a	n/a
39	PAX5	chr12:49390495-49390815	GM12878	blood:	n/a	n/a
40	RAD21	chr12:49390464-49390906	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr12:49390508-49390801	A549	lung:	n/a	n/a
42	CTCF	chr12:49390583-49390810	HepG2	liver:	n/a	n/a
43	CTCF	chr12:49390640-49390790	HUVEC	blood vessel:	n/a	n/a
44	SMC3	chr12:49390507-49391016	SK-N-SH	brain:	n/a	n/a
45	CTCF	chr12:49390580-49390730	GM12869	blood:	n/a	n/a
46	RAD21	chr12:49390496-49390884	IMR90	lung:	n/a	n/a
47	RUNX3	chr12:49390551-49390852	GM12878	blood:	n/a	n/a
48	CTCF	chr12:49390548-49390841	GM10266	blood:	n/a	n/a
49	CTCF	chr12:49390590-49390789	SK-N-SH_RA	brain:	n/a	n/a
50	CTCF	chr12:49390487-49390872	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:49349835..49352133-chr12:49390670..49393580,2	K562	blood:
2	chr12:49211500..49213760-chr12:49389439..49391048,2	MCF-7	breast:
3	chr12:49370672..49373205-chr12:49390197..49394754,4	MCF-7	breast:
4	chr12:49390629..49391181-chr12:49412071..49412946,2	K562	blood:
5	chr12:49349915..49351718-chr12:49389253..49391123,2	MCF-7	breast:
6	chr12:49390613..49392741-chr12:49658198..49660350,2	K562	blood:
7	chr12:49389429..49391969-chr12:49402571..49406442,3	MCF-7	breast:
8	chr12:49389470..49393018-chr12:49447976..49450275,4	K562	blood:
9	chr12:49367970..49369759-chr12:49389429..49392396,2	K562	blood:
10	chr12:49374060..49376020-chr12:49389393..49391563,2	K562	blood:
11	chr12:49390072..49392510-chr12:49759241..49762093,2	K562	blood:
12	chr12:49390603..49394865-chr12:49395546..49401151,4	MCF-7	breast:
13	chr12:49388997..49391311-chr12:49485672..49487857,2	K562	blood:
14	chr12:49350460..49352797-chr12:49389222..49392992,4	MCF-7	breast:
15	chr12:49390223..49391069-chr12:49413217..49414800,4	K562	blood:
16	chr12:49390613..49393583-chr12:49657516..49659698,3	K562	blood:
17	chr12:49388402..49390811-chr12:49410964..49413711,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257913	TF binding region
ENSG00000125084	Chromatin interaction
ENSG00000272822	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000200303	Chromatin interaction
ENSG00000257346	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000134287	Chromatin interaction
ENSG00000181929	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1054442	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.99[ASN][1000 genomes]
rs10747559	0.82[ASN][1000 genomes]
rs10783300	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783301	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10875906	0.96[ASN][1000 genomes]
rs10875908	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875910	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10875911	0.96[ASN][1000 genomes]
rs10875912	0.94[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[ASN][1000 genomes]
rs10875913	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10875914	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.82[TSI][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875915	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168822	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168827	0.96[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168839	0.84[ASW][hapmap];0.96[CEU][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11168850	1.00[JPT][hapmap]
rs1138908	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11614738	0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.92[ASN][1000 genomes]
rs12580349	0.95[CHD][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2117029	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2241726	0.92[CEU][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2293445	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2293446	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2304275	0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs34436857	0.86[ASN][1000 genomes]
rs3741619	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[ASN][1000 genomes]
rs3741622	0.89[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs3782357	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6580698	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs6580699	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs7296288	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7969091	0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs876333	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription 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 target site	87 gene(s)	inside rSNPs	diseases
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
4	nsv558833	chr12:49358880-49478812	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10783299	DDN	cis	Muscle Skeletal	GTEx
rs10783299	NCKAP5L	cis	parietal	SCAN
rs10783299	RP11-386G11.3	cis	Muscle Skeletal	GTEx
rs10783299	RHEBL1	cis	parietal	SCAN
rs10783299	RP11-386G11.5	cis	Muscle Skeletal	GTEx
rs10783299	RHEBL1	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49388200-49393600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr12:49389200-49390800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:49389200-49390800	Weak transcription	Pancreas	Pancrea
4	chr12:49389400-49390800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:49389400-49390800	Bivalent Enhancer	Fetal Muscle Leg	muscle
6	chr12:49389400-49390800	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr12:49389400-49392000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:49389600-49390800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:49389800-49391800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:49389800-49392400	Weak transcription	Hela-S3	cervix
11	chr12:49390200-49390800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
12	chr12:49390200-49391000	Active TSS	Brain Anterior Caudate	brain
13	chr12:49390200-49391600	Bivalent Enhancer	Fetal Heart	heart
14	chr12:49390400-49390800	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr12:49390400-49390800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
16	chr12:49390400-49390800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
17	chr12:49390400-49390800	Enhancers	Liver	Liver
18	chr12:49390400-49390800	Enhancers	K562	blood
19	chr12:49390400-49391000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
20	chr12:49390400-49391000	Bivalent Enhancer	Fetal Intestine Large	intestine
21	chr12:49390400-49391000	Bivalent Enhancer	Fetal Stomach	stomach
22	chr12:49390400-49391000	Bivalent Enhancer	Fetal Thymus	thymus
23	chr12:49390400-49391000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
24	chr12:49390400-49391200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
25	chr12:49390400-49391400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
26	chr12:49390400-49391600	Enhancers	Placenta Amnion	Placenta Amnion
27	chr12:49390400-49391600	Flanking Bivalent TSS/Enh	Dnd41	blood
28	chr12:49390400-49392400	Active TSS	Brain Angular Gyrus	brain
29	chr12:49390400-49392600	Bivalent Enhancer	Fetal Brain Male	brain
30	chr12:49390400-49392600	Bivalent Enhancer	Fetal Lung	lung
31	chr12:49390400-49393000	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
32	chr12:49390400-49393000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:49390400-49393000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
34	chr12:49390400-49393000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
35	chr12:49390600-49390800	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr12:49390600-49390800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
37	chr12:49390600-49390800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
38	chr12:49390600-49390800	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
39	chr12:49390600-49390800	Bivalent/Poised TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr12:49390600-49390800	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:49390600-49390800	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:49390600-49390800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:49390600-49390800	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:49390600-49390800	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr12:49390600-49390800	Active TSS	Brain Cingulate Gyrus	brain
46	chr12:49390600-49390800	Active TSS	Lung	lung
47	chr12:49390600-49390800	Active TSS	Right Ventricle	heart
48	chr12:49390600-49390800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
49	chr12:49390600-49390800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
50	chr12:49390600-49390800	Enhancers	GM12878-XiMat	blood

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