Variant report

Variant	rs399023
Chromosome Location	chr12:50338952-50338953
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50287732..50289351-chr12:50337980..50339700,2	MCF-7	breast:
2	chr12:50338497..50339666-chr12:50360120..50361429,3	MCF-7	breast:
3	chr12:50338925..50340024-chr12:50360474..50361632,7	K562	blood:
4	chr12:50336938..50340319-chr12:50341822..50344338,4	K562	blood:
5	chr12:50334465..50337544-chr12:50338372..50341772,4	K562	blood:
6	chr12:50331211..50335185-chr12:50337113..50339426,3	MCF-7	breast:
7	chr12:50338558..50341156-chr12:50354977..50356831,3	MCF-7	breast:
8	chr12:50169842..50170749-chr12:50338718..50339494,2	K562	blood:
9	chr12:50261163..50264047-chr12:50337700..50340324,2	MCF-7	breast:
10	chr12:50338638..50340255-chr12:50342218..50344321,2	K562	blood:
11	chr12:50302479..50304923-chr12:50336805..50339549,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000086159	Chromatin interaction
ENSG00000257588	Chromatin interaction
ENSG00000161798	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11169225	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12372344	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759124	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759129	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377470	0.82[EUR][1000 genomes]
rs3782319	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299924	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv832407	chr12:50243268-50412236	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv558835	chr12:50275137-50433234	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription 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	36 gene(s)	inside rSNPs	diseases
7	nsv899072	chr12:50326176-50379667	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899073	chr12:50335628-50360461	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50334000-50339200	Weak transcription	Lung	lung
2	chr12:50335600-50339200	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr12:50336000-50339200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:50336200-50339800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:50336200-50340000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr12:50336400-50339800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:50336600-50339200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:50337200-50339000	Weak transcription	Gastric	stomach
9	chr12:50337200-50339200	Weak transcription	Colonic Mucosa	Colon
10	chr12:50337200-50339200	Weak transcription	HMEC	breast
11	chr12:50337200-50339400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:50337400-50339200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:50337400-50339200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:50337400-50339200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:50337400-50339200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:50337400-50339200	Weak transcription	NHEK	skin
17	chr12:50337600-50339000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:50337800-50339000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:50337800-50339000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
20	chr12:50337800-50339200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:50337800-50339200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:50337800-50339200	Bivalent Enhancer	HepG2	liver
23	chr12:50338000-50339200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr12:50338000-50339200	Enhancers	Hela-S3	cervix
25	chr12:50338000-50339600	Enhancers	Pancreas	Pancrea
26	chr12:50338000-50340000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr12:50338000-50340600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:50338200-50339000	Weak transcription	Stomach Mucosa	stomach
29	chr12:50338200-50339200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:50338200-50339200	Weak transcription	Esophagus	oesophagus
31	chr12:50338400-50339000	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr12:50338400-50339200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr12:50338600-50339000	Enhancers	Primary B cells from cord blood	blood
34	chr12:50338600-50339000	Enhancers	Fetal Thymus	thymus
35	chr12:50338600-50339000	Enhancers	Right Atrium	heart
36	chr12:50338600-50339200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:50338600-50339200	Enhancers	Primary T cells fromperipheralblood	blood
38	chr12:50338600-50339200	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr12:50338600-50339200	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr12:50338600-50339200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:50338600-50339400	Enhancers	Left Ventricle	heart
42	chr12:50338800-50339000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
43	chr12:50338800-50339000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
44	chr12:50338800-50339000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:50338800-50339000	Enhancers	Fetal Brain Female	brain
46	chr12:50338800-50339200	Enhancers	H9 Cell Line	embryonic stem cell
47	chr12:50338800-50339200	Enhancers	Primary T cells from cord blood	blood
48	chr12:50338800-50339200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:50338800-50339200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr12:50338800-50339200	Enhancers	Thymus	Thymus

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