Variant report

Variant	rs1560010
Chromosome Location	chr12:9811058-9811059
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9810242..9813132-chr12:9813704..9817912,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000069493	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10772005	0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs10772006	0.94[YRI][hapmap];0.83[AFR][1000 genomes]
rs10844327	0.84[AFR][1000 genomes]
rs10844350	0.95[YRI][hapmap];0.90[AFR][1000 genomes]
rs10844351	0.95[YRI][hapmap];0.90[AFR][1000 genomes]
rs10844352	0.90[AFR][1000 genomes]
rs10844353	0.90[AFR][1000 genomes]
rs10844359	0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs10844369	0.84[AFR][1000 genomes]
rs11052245	0.90[AFR][1000 genomes]
rs11052274	1.00[CEU][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11830731	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12310789	0.83[AFR][1000 genomes]
rs12322854	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1560008	0.87[AFR][1000 genomes]
rs1560009	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16909916	0.91[EUR][1000 genomes]
rs16913477	0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs16914229	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16914557	0.96[EUR][1000 genomes]
rs2114869	0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs2162657	0.90[AFR][1000 genomes]
rs34333636	0.83[AFR][1000 genomes]
rs35280686	0.90[AFR][1000 genomes]
rs55873283	0.88[AFR][1000 genomes]
rs7132037	0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs7299738	0.90[AFR][1000 genomes]
rs7302746	0.95[YRI][hapmap];0.88[AFR][1000 genomes]
rs7304321	0.90[AFR][1000 genomes]
rs7304464	0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs7305937	0.87[AFR][1000 genomes]
rs7309800	0.95[YRI][hapmap];0.88[AFR][1000 genomes]
rs7310405	0.90[AFR][1000 genomes]
rs7310516	0.90[AFR][1000 genomes]
rs7310568	0.94[YRI][hapmap];0.88[AFR][1000 genomes]
rs7310790	0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs7311421	0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs7311574	0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs7311945	0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs7959406	0.86[AFR][1000 genomes]
rs7959726	0.86[AFR][1000 genomes]
rs7962321	0.94[YRI][hapmap];0.86[AFR][1000 genomes]
rs7973603	0.86[AFR][1000 genomes]
rs7974871	0.94[YRI][hapmap];0.83[AFR][1000 genomes]
rs7978187	0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs958340	0.86[AFR][1000 genomes]
rs9919714	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9919787	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS 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	18 gene(s)	inside rSNPs	diseases
7	nsv917178	chr12:9637315-9820153	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9801600-9811200	Weak transcription	Gastric	stomach
2	chr12:9801600-9815600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:9802200-9815200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:9802400-9849800	Weak transcription	Pancreas	Pancrea
5	chr12:9802600-9812800	Weak transcription	Ovary	ovary
6	chr12:9802600-9814400	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:9803000-9811200	Weak transcription	Fetal Intestine Small	intestine
8	chr12:9803000-9812200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr12:9803000-9816400	Weak transcription	Brain Germinal Matrix	brain
10	chr12:9803000-9816800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:9803000-9819800	Weak transcription	Fetal Brain Female	brain
12	chr12:9803000-9820200	Weak transcription	Brain Substantia Nigra	brain
13	chr12:9803000-9822200	Weak transcription	Small Intestine	intestine
14	chr12:9803200-9812400	Weak transcription	Liver	Liver
15	chr12:9803200-9813400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:9803600-9812200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:9803600-9826200	Weak transcription	Esophagus	oesophagus
18	chr12:9804000-9814200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr12:9804200-9811200	Weak transcription	Right Ventricle	heart
20	chr12:9804200-9812400	Weak transcription	Brain Anterior Caudate	brain
21	chr12:9804200-9813200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr12:9804200-9814200	Weak transcription	Colonic Mucosa	Colon
23	chr12:9804200-9814600	Weak transcription	Lung	lung
24	chr12:9804200-9815000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr12:9804400-9811200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:9804400-9811200	Weak transcription	Fetal Stomach	stomach
27	chr12:9804400-9811200	Weak transcription	Spleen	Spleen
28	chr12:9804400-9812200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr12:9804400-9812200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr12:9804400-9812200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:9804400-9814600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:9804400-9820400	Weak transcription	HUVEC	blood vessel
33	chr12:9804600-9820000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:9804600-9820000	Weak transcription	HMEC	breast
35	chr12:9804600-9820200	Weak transcription	NHEK	skin
36	chr12:9804800-9811200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr12:9805000-9813800	Weak transcription	K562	blood
38	chr12:9805600-9813600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
39	chr12:9805600-9815000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr12:9805600-9819400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:9805800-9818200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:9806000-9813400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr12:9806000-9813400	Weak transcription	Fetal Brain Male	brain
44	chr12:9806000-9814400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:9806000-9814800	Strong transcription	Fetal Thymus	thymus
46	chr12:9806000-9815400	Strong transcription	Fetal Intestine Large	intestine
47	chr12:9806000-9818000	Strong transcription	Fetal Muscle Leg	muscle
48	chr12:9806200-9814200	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr12:9806200-9815800	Strong transcription	Fetal Muscle Trunk	muscle
50	chr12:9806200-9818200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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