Variant report

Variant	rs12476008
Chromosome Location	chr2:9755388-9755389
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:9750980-9757087	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:42142647..42144954-chr2:9753163..9755825,2	MCF-7	breast:
2	chr2:9694040..9697595-chr2:9752237..9755817,4	MCF-7	breast:
3	chr2:9752399..9758466-chr2:9767981..9772630,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000207086	TF binding region
ENSG00000151694	Chromatin interaction
ENSG00000271855	Chromatin interaction
ENSG00000161654	Chromatin interaction
ENSG00000134308	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11674777	1.00[JPT][hapmap]
rs11888902	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11890807	1.00[JPT][hapmap]
rs11902264	1.00[JPT][hapmap]
rs11902431	0.92[EUR][1000 genomes]
rs12465158	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12470619	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12692388	1.00[JPT][hapmap]
rs16867062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16867073	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs16867074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3791748	1.00[JPT][hapmap]
rs41308184	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4669401	0.88[EUR][1000 genomes]
rs62119390	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62119425	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62119430	0.97[EUR][1000 genomes]
rs6432018	1.00[JPT][hapmap]
rs6432023	1.00[JPT][hapmap]
rs6432025	1.00[JPT][hapmap]
rs6715408	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6734469	1.00[JPT][hapmap]
rs7569485	1.00[JPT][hapmap]
rs7597961	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[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
rs12476008	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	chr2:9741400-9760000	Weak transcription	Fetal Kidney	kidney
3	chr2:9742200-9757000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:9742800-9757800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:9744800-9766800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:9747800-9760200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:9748000-9757000	Enhancers	Brain Hippocampus Middle	brain
8	chr2:9748600-9756400	Enhancers	Brain Substantia Nigra	brain
9	chr2:9748600-9765600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr2:9748600-9766600	Weak transcription	Aorta	Aorta
11	chr2:9748600-9767600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:9748800-9758800	Weak transcription	Thymus	Thymus
13	chr2:9748800-9761200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:9748800-9763400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr2:9749000-9756800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr2:9749000-9757800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:9749000-9764600	Weak transcription	Lung	lung
18	chr2:9749000-9769200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr2:9749200-9764000	Weak transcription	Fetal Brain Male	brain
20	chr2:9749200-9768000	Weak transcription	Stomach Mucosa	stomach
21	chr2:9749400-9762800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:9749600-9758000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr2:9749600-9768200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr2:9750000-9755800	Weak transcription	Brain Germinal Matrix	brain
25	chr2:9750000-9755800	Strong transcription	Dnd41	blood
26	chr2:9750000-9758000	Weak transcription	HUVEC	blood vessel
27	chr2:9750200-9758400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:9750200-9758600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr2:9750400-9756000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:9750800-9756400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:9751000-9757000	Enhancers	Colon Smooth Muscle	Colon
32	chr2:9751000-9757000	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr2:9751000-9759000	Genic enhancers	A549	lung
34	chr2:9751600-9756000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:9751600-9758800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr2:9751800-9756200	Enhancers	Fetal Heart	heart
37	chr2:9751800-9758800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:9752200-9757000	Enhancers	Brain Angular Gyrus	brain
39	chr2:9752200-9757200	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr2:9752200-9757800	Weak transcription	Left Ventricle	heart
41	chr2:9752200-9762200	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr2:9752200-9768200	Weak transcription	Colonic Mucosa	Colon
43	chr2:9752400-9755600	Enhancers	Brain Cingulate Gyrus	brain
44	chr2:9752400-9758800	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr2:9752600-9756400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr2:9752800-9756200	Enhancers	Brain Anterior Caudate	brain
47	chr2:9752800-9757000	Weak transcription	Fetal Muscle Leg	muscle
48	chr2:9753000-9755400	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr2:9753000-9756600	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr2:9753000-9757400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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