Variant report

Variant	rs11709054
Chromosome Location	chr3:42786020-42786021
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42622067..42623829-chr3:42785959..42788235,2	K562	blood:
2	chr3:42613463..42614205-chr3:42785557..42786369,3	MCF-7	breast:
3	chr3:42785917..42786497-chr3:42922204..42923133,2	K562	blood:

Variant related genes	Relation type
ENSG00000008324	Chromatin interaction
ENSG00000093183	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10461012	0.92[EUR][1000 genomes]
rs10865920	0.95[EUR][1000 genomes]
rs10865921	0.95[EUR][1000 genomes]
rs10865923	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11129969	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11129970	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709500	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713172	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11915803	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17074778	0.95[EUR][1000 genomes]
rs17238314	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17238798	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2240861	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34110933	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682856	0.89[EUR][1000 genomes]
rs55884426	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55904344	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59478814	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59713146	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60049195	0.95[EUR][1000 genomes]
rs60176972	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62246603	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62246606	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62246635	0.88[EUR][1000 genomes]
rs62250113	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62250114	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6442057	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72865716	0.97[ASN][1000 genomes]
rs9836162	0.93[EUR][1000 genomes]
rs9837412	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9838388	0.85[EUR][1000 genomes]
rs9880635	0.81[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	nsv1013578	chr3:42747858-42817321	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv999713	chr3:42749022-42817321	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42769800-42787600	Weak transcription	Gastric	stomach
2	chr3:42776800-42787000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:42778000-42811000	Weak transcription	Spleen	Spleen
4	chr3:42778200-42788000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:42778400-42786400	Weak transcription	Right Ventricle	heart
6	chr3:42781000-42788600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr3:42781200-42787400	Weak transcription	Aorta	Aorta
8	chr3:42781200-42788600	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr3:42781600-42787400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:42781800-42802800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:42782400-42787400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:42783600-42786400	Weak transcription	Psoas Muscle	Psoas
13	chr3:42784600-42787400	Weak transcription	Left Ventricle	heart
14	chr3:42785200-42787400	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr3:42785200-42790200	Enhancers	Brain Anterior Caudate	brain
16	chr3:42785200-42792000	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr3:42785200-42792000	Enhancers	Brain Substantia Nigra	brain
18	chr3:42785400-42787800	Enhancers	Colon Smooth Muscle	Colon
19	chr3:42785400-42787800	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr3:42785400-42788800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:42785400-42790200	Enhancers	Brain Hippocampus Middle	brain
22	chr3:42785400-42792000	Enhancers	Brain Cingulate Gyrus	brain
23	chr3:42785600-42786200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:42785600-42787200	Enhancers	Stomach Smooth Muscle	stomach
25	chr3:42785600-42787400	Enhancers	HepG2	liver
26	chr3:42785600-42790200	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr3:42785600-42791600	Enhancers	Rectal Smooth Muscle	rectum
28	chr3:42785600-42791800	Enhancers	Primary T cells fromperipheralblood	blood
29	chr3:42785800-42786200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:42785800-42786200	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr3:42785800-42786200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:42785800-42786200	Enhancers	Adipose Nuclei	Adipose
33	chr3:42785800-42786400	Weak transcription	Fetal Stomach	stomach
34	chr3:42785800-42786600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr3:42785800-42786600	Weak transcription	Brain Angular Gyrus	brain
36	chr3:42785800-42786600	Weak transcription	Right Atrium	heart
37	chr3:42785800-42787000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:42785800-42787400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:42785800-42787800	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr3:42785800-42788000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:42785800-42791800	Enhancers	Fetal Muscle Leg	muscle
42	chr3:42786000-42786200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr3:42786000-42786800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr3:42786000-42787000	Weak transcription	Fetal Heart	heart
45	chr3:42786000-42787800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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