Variant report

Variant	rs12655052
Chromosome Location	chr5:36149661-36149662
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	chr5:36142364..36144449-chr5:36149144..36153081,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164187	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10512648	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10941274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655033	0.88[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[ASN][1000 genomes]
rs12655301	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12657634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16902727	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2270909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs267786	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs267790	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28362652	0.95[ASN][1000 genomes]
rs28362653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33674	0.89[CHB][hapmap]
rs35071851	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35708472	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3804440	1.00[ASW][hapmap];0.81[MEX][hapmap]
rs4869459	1.00[ASW][hapmap]
rs4869463	0.83[ASN][1000 genomes]
rs4869465	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4869615	1.00[ASW][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes]
rs4869622	1.00[ASW][hapmap];0.81[MEX][hapmap]
rs71617744	0.86[AMR][1000 genomes];0.95[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	nsv830262	chr5:36074311-36293872	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	63 gene(s)	inside rSNPs	diseases
2	nsv4795	chr5:36106115-36150407	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36101200-36150800	Weak transcription	Colonic Mucosa	Colon
2	chr5:36108400-36150600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr5:36117400-36150200	Weak transcription	Colon Smooth Muscle	Colon
4	chr5:36126800-36150400	Weak transcription	Fetal Heart	heart
5	chr5:36128200-36150800	Weak transcription	Psoas Muscle	Psoas
6	chr5:36132600-36150800	Weak transcription	Right Ventricle	heart
7	chr5:36134200-36150400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:36136600-36150200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:36136600-36150600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr5:36136600-36150600	Weak transcription	HSMMtube	muscle
11	chr5:36139000-36150600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr5:36140400-36150600	Weak transcription	NHLF	lung
13	chr5:36140600-36150400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr5:36140600-36150600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr5:36140600-36150600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:36140600-36150600	Weak transcription	Thymus	Thymus
17	chr5:36140600-36150800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:36140600-36150800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:36140600-36150800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:36140600-36150800	Weak transcription	Aorta	Aorta
21	chr5:36140600-36150800	Weak transcription	Brain Angular Gyrus	brain
22	chr5:36140600-36150800	Weak transcription	Gastric	stomach
23	chr5:36140600-36150800	Weak transcription	Small Intestine	intestine
24	chr5:36140600-36150800	Weak transcription	Spleen	Spleen
25	chr5:36140600-36151000	Weak transcription	Esophagus	oesophagus
26	chr5:36140600-36151000	Weak transcription	Left Ventricle	heart
27	chr5:36140600-36151000	Weak transcription	Pancreas	Pancrea
28	chr5:36140600-36151200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:36140600-36151200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr5:36140800-36150200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr5:36140800-36150400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr5:36140800-36150600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:36140800-36150600	Weak transcription	Brain Anterior Caudate	brain
34	chr5:36140800-36150600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr5:36140800-36150600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr5:36140800-36150800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr5:36140800-36150800	Weak transcription	Fetal Lung	lung
38	chr5:36140800-36150800	Weak transcription	Fetal Stomach	stomach
39	chr5:36140800-36150800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr5:36140800-36151000	Weak transcription	Lung	lung
41	chr5:36140800-36151000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr5:36141000-36149800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr5:36141000-36150200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr5:36141000-36150200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr5:36141000-36150400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr5:36141000-36150600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr5:36141000-36150600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr5:36141000-36150600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr5:36141000-36150600	Weak transcription	HSMM	muscle
50	chr5:36141000-36150800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links