Variant report

Variant	rs1317263
Chromosome Location	chr12:50032473-50032474
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:50028209-50038752	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:50032183-50033356	K562	blood:	n/a	n/a
3	POLR2A	chr12:50032274-50032700	HUVEC	blood vessel:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50030609..50032918-chr12:50100785..50102656,2	K562	blood:
2	chr12:50030612..50033545-chr12:50151440..50153284,2	K562	blood:
3	chr12:50023902..50034192-chr12:50133489..50138270,11	K562	blood:
4	chr12:50030609..50033291-chr12:50101156..50102921,3	K562	blood:
5	chr12:50025765..50028699-chr12:50032246..50034238,4	K562	blood:
6	chr12:50029309..50033089-chr12:50034924..50039284,4	MCF-7	breast:
7	chr12:50032076..50035986-chr12:50043238..50048000,4	MCF-7	breast:
8	chr12:50024342..50028618-chr12:50029311..50035232,8	K562	blood:

No data

Variant related genes	Relation type
PRPF40B	TF binding region
ENSG00000139644	Chromatin interaction
ENSG00000161791	Chromatin interaction
ENSG00000110844	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10128824	1.00[AMR][1000 genomes]
rs11169110	1.00[AMR][1000 genomes]
rs11169114	1.00[AMR][1000 genomes]
rs11169115	1.00[AMR][1000 genomes]
rs11169120	1.00[AMR][1000 genomes]
rs11169123	1.00[AMR][1000 genomes]
rs12297814	1.00[AMR][1000 genomes]
rs12299477	1.00[AMR][1000 genomes]
rs12299666	1.00[AMR][1000 genomes]
rs12299743	1.00[AMR][1000 genomes]
rs12299751	1.00[AMR][1000 genomes]
rs12300376	0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs12300919	1.00[EUR][1000 genomes]
rs12300962	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12306951	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12310580	1.00[AMR][1000 genomes]
rs12312112	1.00[AMR][1000 genomes]
rs12313657	1.00[AMR][1000 genomes]
rs12313681	1.00[AMR][1000 genomes]
rs12314036	1.00[AMR][1000 genomes]
rs12315508	1.00[AMR][1000 genomes]
rs12316175	1.00[EUR][1000 genomes]
rs12317162	1.00[AMR][1000 genomes]
rs12319527	1.00[AMR][1000 genomes]
rs12320895	1.00[AMR][1000 genomes]
rs17119738	1.00[ASW][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17123724	0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs17123729	1.00[EUR][1000 genomes]
rs17123778	0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs17123787	0.92[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17123827	0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs17123879	1.00[AMR][1000 genomes]
rs17123924	1.00[AMR][1000 genomes]
rs57625108	1.00[EUR][1000 genomes]
rs58039341	1.00[EUR][1000 genomes]
rs61438877	1.00[EUR][1000 genomes]
rs73305101	1.00[EUR][1000 genomes]
rs73306844	1.00[EUR][1000 genomes]
rs73306846	1.00[EUR][1000 genomes]
rs73306864	1.00[EUR][1000 genomes]
rs73306865	1.00[EUR][1000 genomes]
rs73306875	1.00[EUR][1000 genomes]
rs73306891	1.00[EUR][1000 genomes]
rs73309004	1.00[EUR][1000 genomes]
rs73309010	1.00[EUR][1000 genomes]
rs73309013	1.00[EUR][1000 genomes]
rs73309017	1.00[EUR][1000 genomes]
rs73309026	1.00[EUR][1000 genomes]
rs9804867	1.00[AMR][1000 genomes]
rs9805090	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
4	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50017600-50035600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:50017800-50036400	Weak transcription	Colonic Mucosa	Colon
3	chr12:50017800-50042200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:50018000-50035400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:50018000-50035600	Weak transcription	Left Ventricle	heart
6	chr12:50018000-50035800	Weak transcription	HSMMtube	muscle
7	chr12:50018000-50043000	Weak transcription	Psoas Muscle	Psoas
8	chr12:50018200-50033800	Weak transcription	Esophagus	oesophagus
9	chr12:50019000-50038200	Weak transcription	K562	blood
10	chr12:50022000-50036600	Weak transcription	NHDF-Ad	bronchial
11	chr12:50024600-50036400	Weak transcription	Thymus	Thymus
12	chr12:50024800-50035400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:50025200-50035200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:50025400-50033400	Strong transcription	NHEK	skin
15	chr12:50028400-50035400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:50029400-50033800	Weak transcription	Gastric	stomach
17	chr12:50029800-50035600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:50030000-50035600	Weak transcription	HMEC	breast
19	chr12:50030600-50033400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr12:50030800-50032800	Weak transcription	Primary T cells from cord blood	blood
21	chr12:50030800-50033800	Weak transcription	Fetal Brain Female	brain
22	chr12:50030800-50036400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr12:50030800-50038400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr12:50030800-50057000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr12:50031000-50034800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr12:50031000-50035600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr12:50031000-50036000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr12:50031000-50036200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:50031000-50036400	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr12:50031200-50035400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:50031200-50035600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr12:50031200-50035600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr12:50031200-50036200	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr12:50031200-50036800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:50031200-50038200	Weak transcription	Stomach Mucosa	stomach
36	chr12:50031200-50038400	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr12:50031200-50038600	Strong transcription	Fetal Intestine Large	intestine
38	chr12:50031200-50045600	Weak transcription	Small Intestine	intestine
39	chr12:50031400-50032600	Strong transcription	Placenta	Placenta
40	chr12:50031400-50033000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr12:50031400-50033000	Weak transcription	GM12878-XiMat	blood
42	chr12:50031400-50034200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr12:50031400-50034200	Weak transcription	NHLF	lung
44	chr12:50031400-50034800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:50031400-50034800	Weak transcription	Fetal Intestine Small	intestine
46	chr12:50031400-50034800	Weak transcription	Lung	lung
47	chr12:50031400-50035000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr12:50031400-50035600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:50031400-50035600	Weak transcription	Right Ventricle	heart
50	chr12:50031400-50036000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links