Variant report

Variant	rs2131107
Chromosome Location	chr3:49548008-49548009
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49506481..49509131-chr3:49546764..49549304,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DAG1-1	chr3:49547852-49548069	NONHSAT089696

Variant related genes	Relation type
ENSG00000173402	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs11130197	1.00[YRI][hapmap]
rs11130201	1.00[AFR][1000 genomes]
rs11708174	1.00[YRI][hapmap]
rs11717485	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1522929	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1568663	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17080495	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17080510	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17080567	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17080664	0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1996874	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2311794	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2311801	0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2329024	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3870334	0.82[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3870340	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3912831	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4241409	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs4452334	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855856	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855857	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855870	0.89[AFR][1000 genomes]
rs4855872	1.00[EUR][1000 genomes]
rs4855874	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855875	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855876	1.00[EUR][1000 genomes]
rs4855878	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855879	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs55808753	0.89[AFR][1000 genomes]
rs55990645	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56101322	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56760510	1.00[EUR][1000 genomes]
rs56897974	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59579780	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60011446	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61749312	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446269	0.86[AFR][1000 genomes]
rs6446270	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446271	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446273	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446276	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446278	0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs6446279	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446280	0.92[AFR][1000 genomes]
rs6446281	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446282	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446283	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6762593	1.00[YRI][hapmap]
rs6766297	1.00[EUR][1000 genomes]
rs6787665	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6793124	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6797164	1.00[YRI][hapmap]
rs73830703	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73830704	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73830705	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73830706	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831434	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831435	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831436	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831437	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831438	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831439	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831440	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831441	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73831442	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73834006	1.00[AMR][1000 genomes]
rs7646393	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8179172	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9311441	0.89[AFR][1000 genomes]
rs9830627	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9837396	1.00[EUR][1000 genomes]
rs9861805	1.00[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	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49515400-49548800	Weak transcription	Esophagus	oesophagus
2	chr3:49523600-49548200	Weak transcription	Brain Substantia Nigra	brain
3	chr3:49529600-49568600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr3:49538000-49554800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:49538200-49550600	Weak transcription	Colonic Mucosa	Colon
6	chr3:49538600-49548800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:49538800-49553800	Weak transcription	HUVEC	blood vessel
8	chr3:49538800-49554200	Weak transcription	Aorta	Aorta
9	chr3:49539000-49548200	Weak transcription	NH-A	brain
10	chr3:49539000-49550400	Weak transcription	Stomach Mucosa	stomach
11	chr3:49539000-49550400	Weak transcription	NHDF-Ad	bronchial
12	chr3:49539400-49550400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:49539600-49568600	Weak transcription	Small Intestine	intestine
14	chr3:49539800-49548200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:49540000-49548200	Weak transcription	Fetal Heart	heart
16	chr3:49541800-49548400	Weak transcription	Fetal Kidney	kidney
17	chr3:49542000-49553200	Weak transcription	A549	lung
18	chr3:49546200-49577000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr3:49546400-49554400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:49546600-49548800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:49546600-49552000	Strong transcription	Hela-S3	cervix
22	chr3:49546600-49556200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr3:49546600-49556400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:49547000-49550600	Weak transcription	Pancreas	Pancrea
25	chr3:49547000-49572000	Weak transcription	Fetal Brain Male	brain
26	chr3:49547400-49552000	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr3:49547400-49562200	Strong transcription	Primary T cells from cord blood	blood
28	chr3:49547600-49555400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:49547600-49556000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:49547600-49556200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:49547600-49564200	Strong transcription	Fetal Intestine Small	intestine
32	chr3:49547800-49548200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:49547800-49548200	Genic enhancers	Fetal Muscle Trunk	muscle
34	chr3:49547800-49548200	Genic enhancers	Right Ventricle	heart
35	chr3:49547800-49548200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
36	chr3:49547800-49548400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:49547800-49548400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:49547800-49548400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr3:49547800-49548400	Genic enhancers	Colon Smooth Muscle	Colon
40	chr3:49547800-49548600	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:49547800-49549000	Strong transcription	K562	blood
42	chr3:49547800-49549200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:49547800-49549200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:49547800-49549200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:49547800-49549200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr3:49547800-49549200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr3:49547800-49549200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr3:49547800-49549200	Strong transcription	Liver	Liver
49	chr3:49547800-49549200	Strong transcription	Ovary	ovary
50	chr3:49547800-49549200	Strong transcription	NHEK	skin

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