Variant report

Variant	rs12470619
Chromosome Location	chr2:9715208-9715209
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9713260..9716233-chr2:9769016..9771805,2	K562	blood:
2	chr2:9713407..9715979-chr2:9716720..9720102,3	K562	blood:
3	chr2:9714260..9715979-chr2:9716130..9718220,2	K562	blood:
4	chr2:9713407..9715894-chr2:9718602..9720174,2	K562	blood:

Variant related genes	Relation type
ENSG00000134308	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11888902	0.86[EUR][1000 genomes]
rs11902431	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12465158	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476008	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16867062	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16867073	0.90[EUR][1000 genomes]
rs16867074	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41308184	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669401	0.93[EUR][1000 genomes]
rs62119390	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62119425	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62119430	0.90[EUR][1000 genomes]
rs6715408	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597961	0.90[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv580915	chr2:9308148-9844178	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12470619	LOC645233///LOC732360///TDG	trans	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9696800-9719800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:9696800-9767600	Weak transcription	Gastric	stomach
3	chr2:9697000-9720000	Weak transcription	Fetal Stomach	stomach
4	chr2:9697200-9719800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:9697200-9723800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:9697400-9725000	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:9697400-9729800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:9697800-9723600	Weak transcription	Primary B cells from cord blood	blood
9	chr2:9698000-9720000	Weak transcription	Fetal Brain Female	brain
10	chr2:9699600-9725600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:9701000-9720400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:9704600-9719000	Weak transcription	Liver	Liver
13	chr2:9705400-9723600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr2:9705400-9723600	Weak transcription	Colonic Mucosa	Colon
15	chr2:9706000-9722800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:9706000-9722800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:9706000-9733600	Weak transcription	Pancreas	Pancrea
18	chr2:9706200-9720200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr2:9706200-9722800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:9706200-9727800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:9706200-9728000	Weak transcription	Psoas Muscle	Psoas
22	chr2:9706400-9720200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr2:9706400-9723600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:9706400-9725000	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:9706400-9734200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:9710800-9723800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:9711000-9719000	Weak transcription	Right Atrium	heart
28	chr2:9713200-9716000	Enhancers	Fetal Heart	heart
29	chr2:9713400-9723400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:9713600-9722800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:9713600-9723000	Weak transcription	HSMMtube	muscle
32	chr2:9713800-9717200	Weak transcription	K562	blood
33	chr2:9713800-9720000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:9713800-9720400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:9713800-9722000	Weak transcription	NHEK	skin
36	chr2:9713800-9723400	Weak transcription	Hela-S3	cervix
37	chr2:9713800-9723400	Weak transcription	HSMM	muscle
38	chr2:9714000-9720000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:9714000-9723600	Weak transcription	NHLF	lung
40	chr2:9714200-9717800	Weak transcription	Adipose Nuclei	Adipose
41	chr2:9714200-9720000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr2:9714200-9723600	Weak transcription	Brain Substantia Nigra	brain
43	chr2:9714200-9725200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:9714400-9717800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr2:9714400-9718200	Weak transcription	Ovary	ovary
46	chr2:9714400-9720000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:9714400-9720200	Weak transcription	Fetal Muscle Leg	muscle
48	chr2:9714400-9723400	Weak transcription	Placenta	Placenta
49	chr2:9714400-9723400	Weak transcription	HMEC	breast
50	chr2:9714600-9717000	Weak transcription	Fetal Intestine Large	intestine

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