Variant report

Variant	rs12320014
Chromosome Location	chr12:118614021-118614022
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:118612128..118614340-chr12:118811467..118813100,2	MCF-7	breast:
2	chr12:118606761..118609389-chr12:118613397..118615983,2	MCF-7	breast:
3	chr12:118607204..118610139-chr12:118612001..118614626,2	K562	blood:
4	chr12:118613530..118616835-chr12:118807216..118810760,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VSIG10-1	chr12:118613267-118614556	ENSG00000249477

Variant related genes	Relation type
ENSG00000135090	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11068877	1.00[ASW][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap];0.91[YRI][hapmap]
rs11068890	1.00[ASW][hapmap];0.83[LWK][hapmap];0.84[MKK][hapmap]
rs11068895	1.00[ASW][hapmap];0.83[LWK][hapmap];0.84[MKK][hapmap];0.91[YRI][hapmap]
rs11834916	1.00[YRI][hapmap]
rs12300544	0.82[ASW][hapmap];0.89[LWK][hapmap]
rs12319261	1.00[ASW][hapmap];0.83[YRI][hapmap]
rs5745830	1.00[MEX][hapmap]
rs7136654	1.00[AMR][1000 genomes]
rs7137739	0.80[MKK][hapmap]
rs7139188	1.00[AMR][1000 genomes]
rs7313336	1.00[YRI][hapmap]
rs7956203	0.86[AFR][1000 genomes]
rs7959442	0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7978756	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1054703	chr12:118575000-118638613	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv541611	chr12:118575000-118638613	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1035497	chr12:118599539-118732144	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv541612	chr12:118599539-118732144	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118576000-118619600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr12:118576000-118624000	Weak transcription	Stomach Mucosa	stomach
3	chr12:118584000-118627600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:118585800-118619000	Weak transcription	HepG2	liver
5	chr12:118586200-118619400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:118587600-118619200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:118587800-118620000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:118589600-118619000	Weak transcription	A549	lung
9	chr12:118590400-118617000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:118592600-118619400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:118593200-118619200	Strong transcription	Fetal Brain Female	brain
12	chr12:118593200-118619400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:118593200-118619600	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr12:118598200-118620000	Weak transcription	Hela-S3	cervix
15	chr12:118599800-118625600	Weak transcription	Pancreas	Pancrea
16	chr12:118602200-118619600	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr12:118602200-118619600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr12:118602400-118619600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:118602600-118619600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:118602800-118619600	Strong transcription	Primary T cells from cord blood	blood
21	chr12:118602800-118619600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr12:118603000-118615200	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr12:118603200-118619600	Strong transcription	Brain Anterior Caudate	brain
24	chr12:118603400-118614800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr12:118603400-118616800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:118603600-118625400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr12:118603800-118619400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:118604000-118619600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:118604400-118615000	Strong transcription	Brain Hippocampus Middle	brain
30	chr12:118604400-118617400	Strong transcription	Dnd41	blood
31	chr12:118604400-118619600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:118604400-118619600	Strong transcription	Duodenum Mucosa	Duodenum
33	chr12:118604600-118619200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr12:118604800-118615200	Strong transcription	Liver	Liver
35	chr12:118604800-118619400	Strong transcription	Fetal Intestine Large	intestine
36	chr12:118605400-118619600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:118605600-118617400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:118607000-118619400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:118607000-118619400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:118607000-118619400	Strong transcription	Adipose Nuclei	Adipose
41	chr12:118607200-118614400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:118607200-118614600	Strong transcription	Brain Germinal Matrix	brain
43	chr12:118607200-118617400	Strong transcription	Thymus	Thymus
44	chr12:118607200-118619400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr12:118607200-118619600	Strong transcription	Brain Cingulate Gyrus	brain
46	chr12:118607200-118619600	Strong transcription	Fetal Stomach	stomach
47	chr12:118607200-118619600	Strong transcription	Fetal Thymus	thymus
48	chr12:118607400-118614400	Strong transcription	Placenta	Placenta
49	chr12:118607400-118619200	Strong transcription	Brain Angular Gyrus	brain
50	chr12:118607400-118619200	Strong transcription	Brain Inferior Temporal Lobe	brain

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