Variant report

Variant	rs12528480
Chromosome Location	chr6:13414226-13414227
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13413198..13414739-chr6:13489299..13490913,2	MCF-7	breast:
2	chr6:13408702..13411029-chr6:13413155..13415071,2	MCF-7	breast:
3	chr6:13412824..13415397-chr6:13486120..13488724,2	MCF-7	breast:
4	chr6:13396704..13399515-chr6:13413657..13416189,2	K562	blood:

Variant related genes	Relation type
ENSG00000187461	Chromatin interaction
ENSG00000237786	Chromatin interaction
ENSG00000145990	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12527593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16874132	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16874136	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16874138	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16874139	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16874142	1.00[CHB][hapmap]
rs16874145	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16874149	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16874152	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs16874153	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs16874155	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs1992387	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs511996	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs56676493	0.94[ASN][1000 genomes]
rs61017983	0.94[ASN][1000 genomes]
rs6910199	0.80[EUR][1000 genomes]
rs6914294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6926083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931031	1.00[CHB][hapmap]
rs6936420	1.00[CEU][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs73366922	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73366931	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366933	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366936	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366937	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366941	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366945	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366948	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366949	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366951	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366952	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73366960	0.94[ASN][1000 genomes]
rs73366970	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73725822	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7739372	1.00[CHB][hapmap]
rs7740220	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7740298	1.00[CHB][hapmap]
rs7746830	0.86[EUR][1000 genomes]
rs7750943	0.86[EUR][1000 genomes]
rs7758003	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9370100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13401800-13419000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr6:13405000-13418400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr6:13405000-13421800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:13408600-13414600	Weak transcription	NHEK	skin
5	chr6:13408600-13415800	Enhancers	Liver	Liver
6	chr6:13408600-13422600	Weak transcription	HSMM	muscle
7	chr6:13408800-13415200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:13408800-13419400	Weak transcription	Primary B cells from cord blood	blood
9	chr6:13408800-13420200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:13408800-13423000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:13409200-13414600	Weak transcription	Hela-S3	cervix
12	chr6:13409600-13415400	Enhancers	Brain Angular Gyrus	brain
13	chr6:13410000-13415000	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr6:13410200-13415400	Enhancers	Brain Hippocampus Middle	brain
15	chr6:13410200-13415800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:13410400-13416000	Enhancers	Brain Cingulate Gyrus	brain
17	chr6:13410400-13416400	Enhancers	Right Atrium	heart
18	chr6:13410600-13415600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:13410800-13416000	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr6:13411000-13415800	Enhancers	Psoas Muscle	Psoas
21	chr6:13411000-13415800	Weak transcription	GM12878-XiMat	blood
22	chr6:13411200-13415200	Enhancers	Adipose Nuclei	Adipose
23	chr6:13411400-13415600	Enhancers	Pancreas	Pancrea
24	chr6:13411400-13416200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:13411400-13419600	Weak transcription	Fetal Thymus	thymus
26	chr6:13411400-13421800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:13411600-13424200	Enhancers	Right Ventricle	heart
28	chr6:13412200-13419000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:13412400-13414400	Enhancers	Stomach Mucosa	stomach
30	chr6:13412400-13415400	Enhancers	Fetal Lung	lung
31	chr6:13412400-13415800	Enhancers	Spleen	Spleen
32	chr6:13412600-13414800	Enhancers	HSMMtube	muscle
33	chr6:13412600-13415800	Enhancers	Left Ventricle	heart
34	chr6:13412600-13415800	Enhancers	Lung	lung
35	chr6:13412800-13415400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:13412800-13415400	Enhancers	Gastric	stomach
37	chr6:13412800-13415800	Enhancers	Fetal Heart	heart
38	chr6:13412800-13416800	Enhancers	Brain Substantia Nigra	brain
39	chr6:13413000-13414600	Enhancers	NHLF	lung
40	chr6:13413200-13414400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:13413200-13414400	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr6:13413200-13415000	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr6:13413200-13415000	Enhancers	Brain Anterior Caudate	brain
44	chr6:13413200-13415200	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr6:13413200-13415400	Enhancers	Fetal Stomach	stomach
46	chr6:13413200-13417800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr6:13413400-13414400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:13413400-13414400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr6:13413400-13414400	Enhancers	NH-A	brain
50	chr6:13413400-13414600	Weak transcription	Primary neutrophils fromperipheralblood	blood

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