Variant report

Variant	rs12313336
Chromosome Location	chr12:50418388-50418389
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:50358386..50360982-chr12:50417949..50420523,2	MCF-7	breast:
2	chr12:50417982..50420791-chr12:50450221..50452010,2	MCF-7	breast:
3	chr12:50235029..50238212-chr12:50416884..50420841,4	K562	blood:
4	chr12:50410558..50416843-chr12:50417238..50421054,9	MCF-7	breast:
5	chr12:50235029..50237749-chr12:50416744..50419038,3	K562	blood:
6	chr12:50418289..50419175-chr16:72127500..72128244,2	Hela-S3	cervix:
7	chr12:50416797..50419367-chr12:50793748..50795984,3	K562	blood:
8	chr12:50410622..50412312-chr12:50416219..50419390,3	MCF-7	breast:
9	chr12:50418073..50421025-chr12:50559963..50562659,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000161800	Chromatin interaction
ENSG00000110881	Chromatin interaction
ENSG00000186666	Chromatin interaction
ENSG00000139624	Chromatin interaction
ENSG00000086159	Chromatin interaction
ENSG00000140830	Chromatin interaction
ENSG00000161813	Chromatin interaction
ENSG00000140829	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10219607	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11169238	0.87[ASN][1000 genomes]
rs11169252	0.93[ASN][1000 genomes]
rs11503902	0.87[ASN][1000 genomes]
rs12313701	1.00[ASN][1000 genomes]
rs12322177	0.87[ASN][1000 genomes]
rs2292721	0.87[ASN][1000 genomes]
rs296748	0.87[ASN][1000 genomes]
rs296749	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs296758	1.00[JPT][hapmap]
rs56773627	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs58424082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61147017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73297484	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73297487	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73297491	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7972448	1.00[AFR][1000 genomes];1.00[AMR][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	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
4	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
5	nsv469374	chr12:50349765-50467769	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv469375	chr12:50349765-50467769	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS 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	28 gene(s)	inside rSNPs	diseases
7	nsv558837	chr12:50349765-50467769	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active 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	28 gene(s)	inside rSNPs	diseases
8	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50403000-50418600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:50409200-50418400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr12:50409800-50418400	Weak transcription	Primary T cells from cord blood	blood
4	chr12:50410000-50418600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:50410600-50418600	Weak transcription	Spleen	Spleen
6	chr12:50411200-50418600	Weak transcription	Small Intestine	intestine
7	chr12:50411400-50418400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:50411400-50418400	Weak transcription	Brain Hippocampus Middle	brain
9	chr12:50411400-50418400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr12:50411800-50418600	Weak transcription	Esophagus	oesophagus
11	chr12:50412000-50418600	Weak transcription	Lung	lung
12	chr12:50412600-50418400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:50413000-50418600	Weak transcription	Stomach Mucosa	stomach
14	chr12:50415600-50418400	Weak transcription	Brain Substantia Nigra	brain
15	chr12:50415600-50418400	Weak transcription	Colon Smooth Muscle	Colon
16	chr12:50415800-50418400	Weak transcription	HSMMtube	muscle
17	chr12:50416600-50418400	Active TSS	Brain Germinal Matrix	brain
18	chr12:50417200-50418400	Flanking Active TSS	Dnd41	blood
19	chr12:50417600-50418600	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr12:50417600-50418600	Active TSS	Placenta	Placenta
21	chr12:50417600-50419800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:50417800-50418600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:50417800-50418800	Flanking Active TSS	NHEK	skin
24	chr12:50417800-50419600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:50417800-50419600	Active TSS	HSMM	muscle
26	chr12:50417800-50419800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:50418000-50418400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:50418000-50418400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:50418000-50418400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:50418000-50418400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr12:50418000-50418400	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr12:50418000-50418400	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr12:50418000-50418400	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr12:50418000-50418400	Enhancers	Fetal Heart	heart
35	chr12:50418000-50418400	Active TSS	Fetal Thymus	thymus
36	chr12:50418000-50418400	Flanking Active TSS	Hela-S3	cervix
37	chr12:50418000-50418600	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr12:50418000-50418600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr12:50418000-50418600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr12:50418000-50418600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:50418000-50418800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr12:50418000-50418800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:50418000-50418800	Flanking Active TSS	Fetal Lung	lung
44	chr12:50418000-50418800	Flanking Active TSS	HUVEC	blood vessel
45	chr12:50418000-50418800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr12:50418000-50419000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:50418000-50419200	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr12:50418000-50419400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr12:50418000-50419400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr12:50418000-50419400	Active TSS	Fetal Brain Male	brain

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