Variant report

Variant	rs62119425
Chromosome Location	chr2:9737988-9737989
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9735508..9738809-chr2:9769718..9772514,3	MCF-7	breast:
2	chr2:9736847..9738709-chr2:9758595..9761225,2	K562	blood:
3	chr2:9737361..9739506-chr2:9769982..9772140,2	K562	blood:

Variant related genes	Relation type
ENSG00000134308	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11888902	0.89[EUR][1000 genomes]
rs11902431	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12465158	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12470619	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476008	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16867062	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16867073	0.94[EUR][1000 genomes]
rs16867074	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41308184	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669401	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs62119390	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62119430	0.94[EUR][1000 genomes]
rs6715408	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597961	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv214045	chr2:9734039-9742991	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62119425	LOC645233///LOC732360///TDG	trans	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9696800-9767600	Weak transcription	Gastric	stomach
2	chr2:9719200-9747800	Weak transcription	Lung	lung
3	chr2:9723800-9739800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:9726000-9739800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:9728400-9739400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:9728600-9739200	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:9728800-9739200	Weak transcription	Colonic Mucosa	Colon
8	chr2:9729800-9738200	Weak transcription	Thymus	Thymus
9	chr2:9730400-9738400	Weak transcription	Fetal Stomach	stomach
10	chr2:9730600-9738200	Weak transcription	Brain Germinal Matrix	brain
11	chr2:9731800-9738400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:9732200-9738200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:9732200-9738200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:9732200-9738200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr2:9732200-9738200	Weak transcription	Fetal Thymus	thymus
16	chr2:9732200-9738400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:9732200-9738400	Weak transcription	Primary B cells from cord blood	blood
18	chr2:9732200-9738400	Weak transcription	Fetal Kidney	kidney
19	chr2:9732200-9739000	Weak transcription	Liver	Liver
20	chr2:9732200-9739400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr2:9732200-9739400	Weak transcription	Psoas Muscle	Psoas
22	chr2:9732400-9738400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:9732400-9738400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:9732400-9738400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr2:9732400-9747600	Weak transcription	Placenta	Placenta
26	chr2:9732600-9738800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:9732800-9738200	Weak transcription	Fetal Lung	lung
28	chr2:9733400-9738200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr2:9734000-9738200	Weak transcription	Left Ventricle	heart
30	chr2:9734000-9748000	Weak transcription	Pancreas	Pancrea
31	chr2:9734600-9748000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:9735000-9739400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr2:9735200-9738000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:9735200-9738000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr2:9735200-9738200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr2:9735200-9738800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:9735200-9739200	Weak transcription	Brain Angular Gyrus	brain
38	chr2:9735200-9739200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr2:9735200-9748400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr2:9735400-9738200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:9735400-9738200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:9735400-9738400	Weak transcription	Primary T cells from cord blood	blood
43	chr2:9735400-9738400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:9735400-9738400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr2:9735400-9738400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr2:9735400-9739200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:9735400-9739400	Weak transcription	Adipose Nuclei	Adipose
48	chr2:9735400-9739400	Weak transcription	Brain Anterior Caudate	brain
49	chr2:9735400-9739800	Weak transcription	Brain Substantia Nigra	brain
50	chr2:9735400-9748000	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links