Variant report

Variant	rs524939
Chromosome Location	chr13:30531373-30531374
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:30512486..30516242-chr13:30529306..30532066,3	K562	blood:
2	chr13:30423699..30426014-chr13:30530164..30531923,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122042	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10492461	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11838968	1.00[ASN][1000 genomes]
rs11839078	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11839379	0.96[EUR][1000 genomes]
rs11840419	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11840423	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11841787	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11842111	1.00[ASN][1000 genomes]
rs11842198	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11842394	1.00[ASN][1000 genomes]
rs11842819	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547161	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1557088	1.00[ASN][1000 genomes]
rs17074013	1.00[ASN][1000 genomes]
rs17074016	1.00[ASN][1000 genomes]
rs17074063	1.00[ASN][1000 genomes]
rs17074065	1.00[ASN][1000 genomes]
rs17074067	1.00[ASN][1000 genomes]
rs17074166	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17074176	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17587764	1.00[CHB][hapmap]
rs1807336	0.96[EUR][1000 genomes]
rs1998729	1.00[ASN][1000 genomes]
rs4238129	1.00[ASN][1000 genomes]
rs4578499	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4769786	1.00[ASN][1000 genomes]
rs4769787	1.00[ASN][1000 genomes]
rs4769788	1.00[ASN][1000 genomes]
rs4769790	1.00[ASN][1000 genomes]
rs4769791	1.00[ASN][1000 genomes]
rs496557	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525768	0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs552465	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61285944	1.00[ASN][1000 genomes]
rs638278	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs661331	1.00[ASN][1000 genomes]
rs729285	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159369	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159387	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73450320	1.00[ASN][1000 genomes]
rs73450326	1.00[ASN][1000 genomes]
rs73450335	1.00[ASN][1000 genomes]
rs73450337	1.00[ASN][1000 genomes]
rs73450342	1.00[ASN][1000 genomes]
rs73450344	1.00[ASN][1000 genomes]
rs73450347	1.00[ASN][1000 genomes]
rs73450349	1.00[ASN][1000 genomes]
rs73450391	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs745251	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs745252	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9506248	1.00[ASN][1000 genomes]
rs9508600	1.00[ASN][1000 genomes]
rs9508603	1.00[ASN][1000 genomes]
rs9508605	1.00[ASN][1000 genomes]
rs9508611	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9508613	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv510598	chr13:30476386-30542798	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30529600-30531600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr13:30529600-30532200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr13:30529600-30532200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr13:30529600-30532400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr13:30529600-30532400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr13:30529600-30532600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr13:30529600-30538000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr13:30529800-30531600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr13:30529800-30531800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr13:30529800-30532000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr13:30529800-30532200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr13:30529800-30532200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr13:30530600-30532000	Enhancers	Fetal Stomach	stomach
14	chr13:30530600-30533800	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr13:30530600-30534000	Enhancers	H9 Cell Line	embryonic stem cell
16	chr13:30530600-30534000	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr13:30530600-30534000	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr13:30530600-30534000	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr13:30530800-30532200	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr13:30530800-30532400	Enhancers	Fetal Brain Male	brain
21	chr13:30530800-30533600	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr13:30530800-30533800	Enhancers	H1 Cell Line	embryonic stem cell
23	chr13:30531000-30531400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr13:30531000-30531400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr13:30531000-30531400	Flanking Active TSS	Brain Anterior Caudate	brain
26	chr13:30531000-30531400	Bivalent Enhancer	Fetal Lung	lung
27	chr13:30531000-30531600	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr13:30531000-30531600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr13:30531000-30531800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr13:30531000-30531800	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr13:30531000-30531800	Enhancers	Fetal Kidney	kidney
32	chr13:30531000-30532000	Bivalent Enhancer	Fetal Muscle Leg	muscle
33	chr13:30531000-30534200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr13:30531200-30531400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr13:30531200-30531400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr13:30531200-30531400	Flanking Active TSS	Brain Cingulate Gyrus	brain
37	chr13:30531200-30531400	Enhancers	Stomach Smooth Muscle	stomach
38	chr13:30531200-30531600	Weak transcription	Primary T cells from cord blood	blood
39	chr13:30531200-30531600	Flanking Active TSS	Brain Germinal Matrix	brain
40	chr13:30531200-30531600	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr13:30531200-30531600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
42	chr13:30531200-30531800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr13:30531200-30531800	Active TSS	Brain Angular Gyrus	brain
44	chr13:30531200-30531800	Flanking Active TSS	Brain Hippocampus Middle	brain
45	chr13:30531200-30531800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr13:30531200-30532000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr13:30531200-30532200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr13:30531200-30532200	Weak transcription	Primary T helper cells fromperipheralblood	blood

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