Variant report

Variant	rs6542124
Chromosome Location	chr2:113951924-113951925
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:113951006-113952698	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:113951825-113952270	GM12891	blood:	n/a	n/a
3	POLR2A	chr2:113951718-113952660	GM12878	blood:	n/a	n/a
4	POLR2A	chr2:113950972-113952645	GM12891	blood:	n/a	n/a
5	POLR2A	chr2:113951884-113952607	GM12892	blood:	n/a	n/a
6	POLR2A	chr2:113951828-113952665	GM12892	blood:	n/a	n/a
7	PAX5	chr2:113951816-113952229	GM12878	blood:	n/a	n/a
8	CEBPB	chr2:113951889-113952003	HepG2	liver:	n/a	n/a
9	POLR2A	chr2:113949171-113952590	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:113950157..113952055-chr2:113952539..113954758,2	MCF-7	breast:
2	chr2:113950663..113952350-chr2:113953925..113956890,2	K562	blood:
3	chr2:113930203..113932925-chr2:113950004..113952772,2	K562	blood:
4	chr2:113949542..113953586-chr2:113955251..113958622,5	MCF-7	breast:
5	chr2:113949482..113951925-chr2:113952977..113955662,3	K562	blood:
6	chr2:113941477..113944460-chr2:113951684..113956081,4	K562	blood:

No data

Variant related genes	Relation type
PSD4	TF binding region
ENSG00000234174	Chromatin interaction
ENSG00000125637	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs13407583	0.84[EUR][1000 genomes]
rs2305132	0.84[EUR][1000 genomes]
rs6755077	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs68090726	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs752590	0.82[EUR][1000 genomes]
rs7560180	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv582711	chr2:113895516-113984503	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv582712	chr2:113932431-113985170	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv874898	chr2:113935407-113954247	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv874899	chr2:113935407-113962071	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv874900	chr2:113948378-113967990	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113923000-113956000	Weak transcription	HMEC	breast
2	chr2:113934200-113956200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr2:113939400-113956000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:113939400-113956400	Weak transcription	Small Intestine	intestine
5	chr2:113939600-113953800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:113939600-113955400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:113939600-113956200	Weak transcription	Fetal Lung	lung
8	chr2:113940000-113961000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr2:113942800-113956600	Strong transcription	Fetal Thymus	thymus
10	chr2:113942800-113961000	Strong transcription	Dnd41	blood
11	chr2:113943000-113956200	Weak transcription	Brain Substantia Nigra	brain
12	chr2:113943600-113956200	Weak transcription	Adipose Nuclei	Adipose
13	chr2:113943800-113955200	Weak transcription	Stomach Mucosa	stomach
14	chr2:113943800-113956000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:113945600-113952000	Weak transcription	K562	blood
16	chr2:113947400-113961000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr2:113947600-113955800	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr2:113947800-113955200	Strong transcription	Thymus	Thymus
19	chr2:113947800-113956200	Strong transcription	GM12878-XiMat	blood
20	chr2:113947800-113959600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
21	chr2:113947800-113960600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:113948000-113953600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:113948200-113953600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:113948400-113953400	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:113948400-113955000	Strong transcription	Liver	Liver
26	chr2:113948600-113952600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:113948600-113954200	Strong transcription	Colonic Mucosa	Colon
28	chr2:113948600-113955400	Strong transcription	Spleen	Spleen
29	chr2:113948600-113955800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:113948600-113961000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:113948800-113952600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr2:113948800-113955800	Strong transcription	Primary B cells from cord blood	blood
33	chr2:113948800-113955800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:113948800-113955800	Strong transcription	Duodenum Mucosa	Duodenum
35	chr2:113949000-113953800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr2:113949000-113955800	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr2:113949000-113956000	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr2:113949000-113956000	Strong transcription	Primary B cells from peripheral blood	blood
39	chr2:113949000-113961200	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr2:113949600-113954800	Strong transcription	Gastric	stomach
41	chr2:113949800-113955800	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:113950000-113955400	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr2:113950000-113961000	Strong transcription	Primary T cells from cord blood	blood
44	chr2:113950200-113953400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
45	chr2:113950200-113955800	Strong transcription	Primary hematopoietic stem cells	blood
46	chr2:113950400-113954400	Strong transcription	Fetal Intestine Large	intestine
47	chr2:113950600-113955400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr2:113951000-113953200	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr2:113951000-113953400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:113951000-113955400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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