Variant report

Variant	rs6425530
Chromosome Location	chr1:179277602-179277603
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179263909..179265943-chr1:179276676..179278197,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10798655	0.88[ASN][1000 genomes]
rs12725375	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12749666	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2050450	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2050451	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2152318	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2247061	0.98[ASN][1000 genomes]
rs2248979	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2250352	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250477	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254214	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2254580	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2254623	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255375	0.95[AFR][1000 genomes]
rs2257089	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2257100	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2484440	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2484443	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2484446	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492777	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2492778	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2493116	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2493117	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2493118	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2493119	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2783391	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2783392	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2783393	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs404818	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs433722	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4652364	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56371666	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61824366	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7523431	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv990767	chr1:179270152-179277921	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179263800-179304600	Weak transcription	Lung	lung
2	chr1:179263800-179306400	Weak transcription	Gastric	stomach
3	chr1:179264000-179279600	Weak transcription	Fetal Brain Male	brain
4	chr1:179264200-179290200	Weak transcription	Aorta	Aorta
5	chr1:179264600-179278600	Weak transcription	Colonic Mucosa	Colon
6	chr1:179264600-179281200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:179264600-179292000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:179264600-179304600	Weak transcription	Right Ventricle	heart
9	chr1:179264600-179310200	Weak transcription	Brain Substantia Nigra	brain
10	chr1:179264600-179314000	Weak transcription	Brain Angular Gyrus	brain
11	chr1:179264600-179314000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:179264800-179277800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:179264800-179278800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:179264800-179279400	Weak transcription	HSMMtube	muscle
15	chr1:179264800-179313800	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:179264800-179313800	Weak transcription	Fetal Brain Female	brain
17	chr1:179264800-179334200	Weak transcription	Colon Smooth Muscle	Colon
18	chr1:179265400-179287600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:179266400-179286400	Weak transcription	Fetal Kidney	kidney
20	chr1:179266400-179322800	Weak transcription	Small Intestine	intestine
21	chr1:179267800-179287000	Weak transcription	Spleen	Spleen
22	chr1:179268400-179278200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:179268400-179280200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:179268400-179312000	Weak transcription	Fetal Thymus	thymus
25	chr1:179269600-179280000	Weak transcription	Thymus	Thymus
26	chr1:179270200-179283200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:179271000-179279000	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr1:179271400-179287600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr1:179271600-179278200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:179271600-179283800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:179271600-179286400	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:179271800-179280200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:179271800-179287600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:179272000-179284400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:179272000-179286000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:179272600-179288200	Weak transcription	Stomach Mucosa	stomach
37	chr1:179272600-179313800	Weak transcription	Brain Anterior Caudate	brain
38	chr1:179273000-179281400	Weak transcription	Adipose Nuclei	Adipose
39	chr1:179273000-179311600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:179273200-179290400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr1:179273200-179294600	Weak transcription	Placenta	Placenta
42	chr1:179273400-179287000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:179273800-179293400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:179274400-179281200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr1:179274400-179289400	Weak transcription	Fetal Lung	lung
46	chr1:179274600-179278400	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr1:179274600-179281600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:179274600-179284200	Weak transcription	Fetal Intestine Small	intestine
49	chr1:179274600-179302400	Weak transcription	Left Ventricle	heart
50	chr1:179274600-179304400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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