Variant report

Variant	rs3861577
Chromosome Location	chr12:49983135-49983136
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:6)
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	CTCF	chr12:49983101-49983188	H1-hESC	embryonic stem cell:	n/a	n/a
2	GATA1	chr12:49982479-49983267	PBDE	blood:	n/a	chr12:49982618-49982629
3	POLR2A	chr12:49983130-49983285	Hela-S3	cervix:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49981751..49983968-chr5:66846722..66848370,2	MCF-7	breast:
2	chr12:49982198..49984699-chr12:49997127..49999143,2	MCF-7	breast:
3	chr12:49977137..49979191-chr12:49981991..49984278,2	MCF-7	breast:
4	chr12:49982217..49984243-chr12:50003590..50006014,2	MCF-7	breast:
5	chr12:49964375..49969334-chr12:49981796..49986330,5	MCF-7	breast:
6	chr12:49961312..49963172-chr12:49981340..49984293,2	K562	blood:

No data

Variant related genes	Relation type
POLR2KP1	TF binding region
RNU6-834P	TF binding region
ENSG00000110844	Chromatin interaction
ENSG00000187778	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11830472	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs11831670	0.90[AFR][1000 genomes]
rs11831673	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs11831877	0.81[AFR][1000 genomes]
rs11832420	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs11832727	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs11833472	0.96[AFR][1000 genomes]
rs11834570	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs11835085	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs11837399	0.81[AFR][1000 genomes]
rs11837408	0.81[AFR][1000 genomes]
rs11837637	1.00[YRI][hapmap]
rs56840810	0.93[AFR][1000 genomes]
rs57489906	1.00[AFR][1000 genomes]
rs57905415	0.81[AFR][1000 genomes]
rs59597892	0.81[AFR][1000 genomes]
rs59628479	0.81[AFR][1000 genomes]
rs60117004	0.81[AFR][1000 genomes]
rs7131756	0.81[AFR][1000 genomes]
rs7134329	0.81[AFR][1000 genomes]
rs7307183	0.81[AFR][1000 genomes]
rs7310069	1.00[AFR][1000 genomes]
rs7312037	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs7313183	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs7313590	0.81[AFR][1000 genomes]
rs7960185	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs7973011	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7978381	1.00[YRI][hapmap];0.90[AFR][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:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49963000-49984800	Weak transcription	Small Intestine	intestine
2	chr12:49963000-50003200	Weak transcription	Aorta	Aorta
3	chr12:49963200-49986800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:49963400-49984800	Weak transcription	Primary B cells from cord blood	blood
5	chr12:49967800-49987400	Weak transcription	Hela-S3	cervix
6	chr12:49971200-49984800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:49974800-49983400	Weak transcription	Colonic Mucosa	Colon
8	chr12:49974800-49984600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr12:49974800-49984800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr12:49974800-49984800	Weak transcription	Fetal Thymus	thymus
11	chr12:49974800-49985200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:49974800-49985800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr12:49974800-49986200	Weak transcription	K562	blood
14	chr12:49974800-49986600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:49974800-49986600	Weak transcription	NH-A	brain
16	chr12:49975000-49984800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr12:49975000-49986200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr12:49975000-49986400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:49975000-49987000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr12:49975400-49983200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:49976000-49983200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr12:49976800-49984200	Weak transcription	Fetal Intestine Large	intestine
23	chr12:49976800-49994000	Weak transcription	Liver	Liver
24	chr12:49977600-49983200	Genic enhancers	Fetal Muscle Leg	muscle
25	chr12:49977600-49996200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr12:49977800-49984200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr12:49978000-49985000	Weak transcription	Dnd41	blood
28	chr12:49978000-49985400	Weak transcription	Thymus	Thymus
29	chr12:49978000-49988000	Weak transcription	Colon Smooth Muscle	Colon
30	chr12:49978200-49983400	Genic enhancers	Fetal Muscle Trunk	muscle
31	chr12:49978400-49983200	Enhancers	Placenta	Placenta
32	chr12:49978600-49984800	Weak transcription	Ovary	ovary
33	chr12:49978800-49994600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:49979200-49984600	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr12:49979600-49986600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr12:49979600-50002600	Weak transcription	HepG2	liver
37	chr12:49979800-49992000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:49979800-49995600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr12:49979800-49998800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr12:49980000-49984800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:49980000-49988200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr12:49980200-49984800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:49980200-49985400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr12:49980400-49984000	Weak transcription	Fetal Lung	lung
45	chr12:49980400-49987000	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr12:49980400-50000200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:49980600-49983400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:49980600-49984400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:49980800-49984800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:49981000-49984800	Weak transcription	Lung	lung

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