Variant report

Variant	rs56194306
Chromosome Location	chr3:69145516-69145517
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:69142493..69145688-chr3:69155509..69158556,4	MCF-7	breast:
2	chr3:69140755..69142377-chr3:69144139..69146957,2	K562	blood:
3	chr3:69131949..69134135-chr3:69143890..69145665,2	MCF-7	breast:
4	chr3:69128310..69130756-chr3:69144173..69146131,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144746	Chromatin interaction
ENSG00000144744	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1051901	1.00[EUR][1000 genomes]
rs1131960	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12054346	1.00[EUR][1000 genomes]
rs17005366	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3772980	1.00[EUR][1000 genomes]
rs3772983	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3796214	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3821564	1.00[EUR][1000 genomes]
rs56152276	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56280964	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57159802	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58277851	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59090383	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60474520	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61086164	0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs72924853	1.00[EUR][1000 genomes]
rs72924854	1.00[EUR][1000 genomes]
rs73835715	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs73835716	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs73835722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73835726	1.00[EUR][1000 genomes]
rs73835727	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73835728	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73835729	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7617775	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7621394	1.00[EUR][1000 genomes]
rs7621929	1.00[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	nsv876933	chr3:69059023-69227379	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv876934	chr3:69111512-69166895	Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69135200-69155200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:69135800-69155800	Weak transcription	Fetal Kidney	kidney
3	chr3:69136600-69147000	Enhancers	Colon Smooth Muscle	Colon
4	chr3:69136800-69156400	Weak transcription	Fetal Brain Male	brain
5	chr3:69138600-69145600	Enhancers	Stomach Mucosa	stomach
6	chr3:69139800-69145600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:69139800-69154600	Weak transcription	A549	lung
8	chr3:69140000-69147000	Enhancers	Fetal Heart	heart
9	chr3:69140400-69148800	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr3:69141400-69146800	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr3:69141600-69145800	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr3:69141600-69151000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:69141600-69151400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:69141600-69151600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:69141600-69152400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:69141800-69146400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:69141800-69146600	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr3:69141800-69148000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr3:69141800-69150800	Weak transcription	Fetal Lung	lung
20	chr3:69142000-69160400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:69142200-69147200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr3:69142200-69147800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:69142200-69153400	Weak transcription	Fetal Brain Female	brain
24	chr3:69142400-69145600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
25	chr3:69142400-69147200	Genic enhancers	Primary B cells from peripheral blood	blood
26	chr3:69142400-69152200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:69143400-69146600	Enhancers	Brain Substantia Nigra	brain
28	chr3:69143400-69147000	Enhancers	HSMMtube	muscle
29	chr3:69143400-69148800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:69143400-69150800	Genic enhancers	Primary T cells fromperipheralblood	blood
31	chr3:69143600-69145600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:69143600-69145600	Enhancers	K562	blood
33	chr3:69143600-69145800	Enhancers	Rectal Smooth Muscle	rectum
34	chr3:69143600-69146400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:69143600-69147000	Enhancers	Brain Hippocampus Middle	brain
36	chr3:69143600-69147200	Enhancers	Brain Angular Gyrus	brain
37	chr3:69143600-69148600	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr3:69143600-69149000	Weak transcription	Aorta	Aorta
39	chr3:69143600-69149200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr3:69143600-69149200	Weak transcription	Lung	lung
41	chr3:69143600-69150600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:69143600-69150600	Weak transcription	Esophagus	oesophagus
43	chr3:69143600-69151000	Weak transcription	Gastric	stomach
44	chr3:69143600-69151200	Weak transcription	Colonic Mucosa	Colon
45	chr3:69143600-69152600	Weak transcription	Ovary	ovary
46	chr3:69143600-69152800	Weak transcription	Brain Germinal Matrix	brain
47	chr3:69143600-69160200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr3:69143800-69145600	Genic enhancers	Adipose Nuclei	Adipose
49	chr3:69143800-69145800	Genic enhancers	Primary B cells from cord blood	blood
50	chr3:69143800-69146600	Enhancers	HMEC	breast

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