Variant report

Variant	rs12070725
Chromosome Location	chr1:10012146-10012147
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10008573..10013502-chr1:10090291..10096219,9	MCF-7	breast:
2	chr1:10011196..10014061-chr1:10093546..10095391,2	MCF-7	breast:
3	chr1:10003080..10004710-chr1:10011866..10014471,2	K562	blood:

Variant related genes	Relation type
ENSG00000130939	Chromatin interaction
ENSG00000162441	Chromatin interaction
ENSG00000173614	Chromatin interaction

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

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

rs_ID	r²[population]
rs11121501	0.98[AMR][1000 genomes]
rs11121509	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11801898	0.80[ASN][1000 genomes]
rs12058979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12059092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12060375	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12062953	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12064822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12065908	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12071307	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12082318	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12086598	0.98[AMR][1000 genomes]
rs12088598	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12094254	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12097182	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17034440	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2289478	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2297843	0.98[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4845912	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4846104	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4846108	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60132751	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61743470	0.98[AMR][1000 genomes]
rs6663059	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6664208	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7516611	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7535945	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1012301	chr1:9963962-10118393	Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv534853	chr1:9963962-10118393	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv1001742	chr1:9971776-10116767	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv1005461	chr1:9972921-10038862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
9	nsv534855	chr1:9972921-10038862	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 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	chr1:10004000-10034000	Weak transcription	Aorta	Aorta
2	chr1:10004200-10019400	Weak transcription	NH-A	brain
3	chr1:10004200-10021000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:10004200-10033800	Weak transcription	Gastric	stomach
5	chr1:10004400-10018200	Weak transcription	NHLF	lung
6	chr1:10004400-10021200	Weak transcription	HSMM	muscle
7	chr1:10004400-10031600	Weak transcription	Fetal Intestine Large	intestine
8	chr1:10004600-10021000	Weak transcription	HSMMtube	muscle
9	chr1:10004600-10032400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:10004800-10031600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:10004800-10032200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:10004800-10032400	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:10005600-10015000	Strong transcription	Fetal Intestine Small	intestine
14	chr1:10008000-10014200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:10008000-10031800	Weak transcription	Lung	lung
16	chr1:10008000-10032000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:10008000-10032200	Weak transcription	Colonic Mucosa	Colon
18	chr1:10008000-10035000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:10008200-10032000	Weak transcription	Liver	Liver
20	chr1:10008200-10032200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:10008400-10031800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:10008400-10032000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr1:10008400-10032200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:10008600-10031800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:10008600-10033200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:10008600-10035600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:10009000-10013000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr1:10009000-10014200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:10010800-10013600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:10010800-10018600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:10010800-10020400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:10010800-10023000	Weak transcription	HepG2	liver
33	chr1:10010800-10032000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:10010800-10032000	Weak transcription	Thymus	Thymus
35	chr1:10010800-10032200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:10010800-10032600	Weak transcription	Primary T cells from cord blood	blood
37	chr1:10010800-10034800	Weak transcription	NHEK	skin
38	chr1:10010800-10035000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:10010800-10035600	Weak transcription	Fetal Kidney	kidney
40	chr1:10010800-10036400	Weak transcription	Esophagus	oesophagus
41	chr1:10011000-10014200	Weak transcription	Fetal Stomach	stomach
42	chr1:10011000-10014200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr1:10011000-10014400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:10011000-10020600	Weak transcription	Psoas Muscle	Psoas
45	chr1:10011000-10020800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:10011000-10020800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr1:10011000-10021000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr1:10011000-10021000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:10011000-10021600	Weak transcription	Brain Angular Gyrus	brain
50	chr1:10011000-10031800	Weak transcription	Left Ventricle	heart

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