Variant report

Variant	rs11208013
Chromosome Location	chr1:63210900-63210901
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:63201014..63202931-chr1:63208124..63210930,2	MCF-7	breast:
2	chr1:62995947..62996889-chr1:63210716..63211321,2	K562	blood:
3	chr1:62996236..62997976-chr1:63209600..63212359,2	K562	blood:

Variant related genes	Relation type
ENSG00000270549	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10159426	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap];0.82[ASN][1000 genomes]
rs10493327	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs10736399	0.88[ASN][1000 genomes]
rs10749734	0.84[ASN][1000 genomes]
rs10789124	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10789125	0.84[ASN][1000 genomes]
rs10789129	0.84[ASN][1000 genomes]
rs10889366	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889371	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10889372	0.86[ASN][1000 genomes]
rs10889374	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10889375	0.85[ASN][1000 genomes]
rs10889376	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10889383	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[ASN][1000 genomes]
rs10889384	0.80[ASN][1000 genomes]
rs10889386	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11208019	0.85[ASN][1000 genomes]
rs11208023	0.86[ASN][1000 genomes]
rs11208024	0.86[ASN][1000 genomes]
rs11208025	0.87[ASN][1000 genomes]
rs11208026	0.87[ASN][1000 genomes]
rs11208027	0.85[ASN][1000 genomes]
rs11208032	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11208035	0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs11208037	0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs11208038	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11208040	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11208046	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11208047	0.90[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11579171	0.83[ASN][1000 genomes]
rs11587081	1.00[JPT][hapmap]
rs11807368	0.87[ASN][1000 genomes]
rs12085904	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12129919	0.82[ASN][1000 genomes]
rs12138091	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12567340	0.83[ASN][1000 genomes]
rs12567999	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12752360	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1333733	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs1333736	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1360677	0.92[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs1981067	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2149115	0.92[ASN][1000 genomes]
rs2366820	0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs2366821	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2366822	0.80[ASN][1000 genomes]
rs2803238	0.82[GIH][hapmap]
rs2886770	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3211074	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs3737893	0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs4396149	0.87[ASN][1000 genomes]
rs4448545	1.00[JPT][hapmap]
rs6587990	0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs6656747	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6657707	0.82[ASN][1000 genomes]
rs6663165	0.95[CEU][hapmap];0.80[ASN][1000 genomes]
rs6664372	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6664673	0.84[ASN][1000 genomes]
rs6664677	0.86[ASN][1000 genomes]
rs6665455	0.82[ASN][1000 genomes]
rs6670694	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6676637	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6679582	0.88[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[ASN][1000 genomes]
rs6683423	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.82[ASN][1000 genomes]
rs6683832	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6686232	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6687943	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6699457	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6702274	0.88[ASN][1000 genomes]
rs7414021	0.84[ASN][1000 genomes]
rs7517722	0.92[ASN][1000 genomes]
rs7519205	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs7521483	1.00[JPT][hapmap]
rs7540030	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.92[ASN][1000 genomes]
rs7543380	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7546804	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11208013	ATG4C	cis	Thyroid	GTEx
rs11208013	ATG4C///CTR9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:63200200-63212200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:63208800-63220400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr1:63210000-63211200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:63210000-63212000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:63210400-63211000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:63210400-63211000	Enhancers	Colon Smooth Muscle	Colon
7	chr1:63210400-63211200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr1:63210400-63211200	Enhancers	Brain Hippocampus Middle	brain
9	chr1:63210400-63211200	Enhancers	NHDF-Ad	bronchial
10	chr1:63210400-63211400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:63210600-63211000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:63210600-63211000	Enhancers	Brain Substantia Nigra	brain
13	chr1:63210600-63211000	Enhancers	Fetal Muscle Leg	muscle
14	chr1:63210600-63211000	Enhancers	Rectal Smooth Muscle	rectum
15	chr1:63210600-63211000	Enhancers	Stomach Mucosa	stomach
16	chr1:63210600-63211200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:63210600-63211200	Enhancers	Adipose Nuclei	Adipose
18	chr1:63210600-63211200	Enhancers	Fetal Stomach	stomach
19	chr1:63210600-63211200	Enhancers	Ovary	ovary
20	chr1:63210600-63211200	Enhancers	Osteobl	bone
21	chr1:63210800-63211000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:63210800-63211000	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr1:63210800-63211400	Enhancers	HepG2	liver
24	chr1:63210800-63212000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:63210800-63212000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:63210800-63215400	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links