Variant report

Variant	rs12654057
Chromosome Location	chr5:115710778-115710779
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	chr5:115704428..115706706-chr5:115709540..115711421,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10044332	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1090076	0.93[JPT][hapmap]
rs11241386	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12651749	0.80[EUR][1000 genomes]
rs12653124	0.83[CEU][hapmap];0.83[YRI][hapmap]
rs12656608	0.95[ASN][1000 genomes]
rs1351136	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1351137	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs153614	0.83[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs168833	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs17139649	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17139652	0.96[ASN][1000 genomes]
rs17139715	0.83[AFR][1000 genomes]
rs187591	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs194182	0.91[CEU][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap]
rs1991446	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs253953	0.85[ASN][1000 genomes]
rs253956	0.81[ASN][1000 genomes]
rs253960	0.91[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap]
rs27500	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28125	0.91[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap]
rs37182	0.91[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap]
rs3844070	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72808983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs784482	0.89[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap]
rs785368	0.83[CEU][hapmap]
rs804141	0.88[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs804142	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34146	chr5:115315944-115729919	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv2755349	chr5:115384101-115733101	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1017983	chr5:115578765-115713688	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv4968	chr5:115635771-115714856	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv2763489	chr5:115693166-115733327	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115685000-115721400	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr5:115695800-115714600	Weak transcription	Thymus	Thymus
3	chr5:115697600-115712000	Weak transcription	Aorta	Aorta
4	chr5:115697600-115714000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:115697600-115748400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr5:115698000-115722800	Weak transcription	Pancreas	Pancrea
7	chr5:115698400-115714000	Weak transcription	Right Ventricle	heart
8	chr5:115705200-115713000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr5:115706000-115724400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:115706800-115711600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr5:115706800-115723200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr5:115707200-115711800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr5:115707200-115712800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:115707200-115717000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr5:115707400-115711200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:115707400-115711600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:115707400-115714400	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr5:115707400-115717200	Weak transcription	Primary T cells from cord blood	blood
19	chr5:115707400-115722600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr5:115707600-115713200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:115707600-115748400	Weak transcription	Fetal Intestine Large	intestine
22	chr5:115708000-115713400	Weak transcription	Fetal Kidney	kidney
23	chr5:115708200-115714600	Enhancers	Psoas Muscle	Psoas
24	chr5:115708200-115717400	Weak transcription	HUVEC	blood vessel
25	chr5:115708400-115713000	Weak transcription	Brain Hippocampus Middle	brain
26	chr5:115708400-115722400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr5:115708600-115711200	Weak transcription	HepG2	liver
28	chr5:115708600-115711600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr5:115708600-115711600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr5:115708600-115713400	Weak transcription	Lung	lung
31	chr5:115708600-115718000	Weak transcription	Fetal Intestine Small	intestine
32	chr5:115708600-115754000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr5:115708800-115711200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:115708800-115711600	Weak transcription	Brain Anterior Caudate	brain
35	chr5:115708800-115720000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr5:115708800-115722400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr5:115709200-115710800	Weak transcription	Fetal Muscle Leg	muscle
38	chr5:115709400-115722800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr5:115710000-115713000	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr5:115710200-115710800	Enhancers	Adipose Nuclei	Adipose
41	chr5:115710200-115710800	Enhancers	Right Atrium	heart
42	chr5:115710200-115711200	Strong transcription	Primary B cells from cord blood	blood
43	chr5:115710400-115712200	Weak transcription	Brain Angular Gyrus	brain
44	chr5:115710400-115714000	Weak transcription	Esophagus	oesophagus
45	chr5:115710400-115718000	Weak transcription	Spleen	Spleen
46	chr5:115710600-115711200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr5:115710600-115711600	Weak transcription	Left Ventricle	heart

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