Variant report

Variant	rs13906
Chromosome Location	chr12:49952394-49952395
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49758102..49760925-chr12:49950793..49953218,2	MCF-7	breast:
2	chr12:49750823..49752635-chr12:49950607..49952469,2	MCF-7	breast:
3	chr12:49949405..49950994-chr12:49951918..49953792,2	K562	blood:
4	chr12:49933783..49936509-chr12:49951821..49953726,3	K562	blood:

Variant related genes	Relation type
ENSG00000123352	Chromatin interaction
ENSG00000135519	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10219602	1.00[CHB][hapmap]
rs1049986	0.81[ASN][1000 genomes]
rs1078216	1.00[CHB][hapmap]
rs10875964	0.83[ASN][1000 genomes]
rs10875968	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs11169063	0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs11169065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169070	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169076	1.00[CEU][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169080	0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs11169081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169097	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[ASN][1000 genomes]
rs11169101	0.86[JPT][hapmap]
rs11169104	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11169106	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[ASN][1000 genomes]
rs11169109	0.83[ASN][1000 genomes]
rs11169111	0.83[ASN][1000 genomes]
rs11169112	0.83[ASN][1000 genomes]
rs11169118	0.83[ASN][1000 genomes]
rs11169125	0.88[CEU][hapmap];0.85[YRI][hapmap]
rs11169127	0.88[CEU][hapmap];0.81[YRI][hapmap]
rs11169128	1.00[CHB][hapmap]
rs11169130	1.00[CHB][hapmap]
rs11169133	0.83[ASN][1000 genomes]
rs1150057	0.85[JPT][hapmap]
rs11833411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11834380	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[ASN][1000 genomes]
rs12296586	0.83[ASN][1000 genomes]
rs12299505	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[ASN][1000 genomes]
rs12299513	0.94[ASN][1000 genomes]
rs12303310	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12306114	1.00[CHB][hapmap]
rs12308256	0.81[ASN][1000 genomes]
rs12310510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[ASN][1000 genomes]
rs12311527	0.94[ASN][1000 genomes]
rs12311839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12314795	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.83[ASN][1000 genomes]
rs12314878	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12315224	0.83[ASN][1000 genomes]
rs12315791	0.83[ASN][1000 genomes]
rs12316284	0.81[ASN][1000 genomes]
rs12317646	0.83[ASN][1000 genomes]
rs12320556	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1470906	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1574326	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[ASN][1000 genomes]
rs17123808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1902329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1902330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2005195	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241418	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278070	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2303305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2336058	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[ASN][1000 genomes]
rs2878532	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs35275181	1.00[CHB][hapmap]
rs3815832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3887727	0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs3887728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4045193	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4073998	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs4133070	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[ASN][1000 genomes]
rs4563	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[ASN][1000 genomes]
rs4584654	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[ASN][1000 genomes]
rs4993294	1.00[CHB][hapmap]
rs52824916	0.97[ASN][1000 genomes]
rs55853522	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57191490	0.80[ASN][1000 genomes]
rs57342147	0.83[ASN][1000 genomes]
rs57916875	0.97[ASN][1000 genomes]
rs58278271	0.91[ASN][1000 genomes]
rs59233136	0.81[ASN][1000 genomes]
rs59940006	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60121503	0.80[ASN][1000 genomes]
rs61512987	0.84[ASN][1000 genomes]
rs61620972	0.83[ASN][1000 genomes]
rs61710637	0.83[ASN][1000 genomes]
rs6580719	0.83[ASN][1000 genomes]
rs7131915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132792	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7136052	0.83[ASN][1000 genomes]
rs7136772	1.00[CHB][hapmap]
rs7137976	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[ASN][1000 genomes]
rs7296281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299002	0.83[ASN][1000 genomes]
rs7301209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309607	0.81[ASN][1000 genomes]
rs7312658	0.81[ASN][1000 genomes]
rs7313738	0.83[ASN][1000 genomes]
rs73305008	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73305012	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73305085	0.81[ASN][1000 genomes]
rs73305098	0.83[ASN][1000 genomes]
rs73306808	0.83[ASN][1000 genomes]
rs74089182	0.80[ASN][1000 genomes]
rs7688	0.81[ASN][1000 genomes]
rs7952734	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7952938	0.86[ASN][1000 genomes]
rs7953911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[ASN][1000 genomes]
rs7955586	0.81[ASN][1000 genomes]
rs7956089	0.83[ASN][1000 genomes]
rs7956181	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7962645	0.83[ASN][1000 genomes]
rs7962863	0.85[JPT][hapmap]
rs7963954	0.85[JPT][hapmap]
rs7965658	1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs7967624	0.81[ASN][1000 genomes]
rs7970241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979262	0.87[CEU][hapmap];0.81[YRI][hapmap];0.83[ASN][1000 genomes]
rs7979285	0.89[ASN][1000 genomes]
rs7980979	0.83[ASN][1000 genomes]
rs8626	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs876889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs897056	0.81[ASN][1000 genomes]
rs933738	0.94[ASN][1000 genomes]
rs9804749	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv899071	chr12:49927148-49955935	Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49943200-49959600	Weak transcription	Right Atrium	heart
2	chr12:49943400-49952600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:49944800-49952400	Weak transcription	Fetal Kidney	kidney
4	chr12:49945000-49952400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:49946000-49960200	Weak transcription	Fetal Brain Male	brain
6	chr12:49946200-49952400	Weak transcription	HMEC	breast
7	chr12:49946200-49955600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:49946800-49952800	Weak transcription	HUVEC	blood vessel
9	chr12:49947000-49952600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr12:49947200-49956000	Weak transcription	Fetal Heart	heart
11	chr12:49947800-49952400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr12:49947800-49952400	Weak transcription	NH-A	brain
13	chr12:49948200-49960400	Strong transcription	Fetal Brain Female	brain
14	chr12:49948200-49960400	Strong transcription	Fetal Intestine Small	intestine
15	chr12:49948400-49952800	Weak transcription	HSMM	muscle
16	chr12:49948600-49952400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr12:49949000-49953400	Weak transcription	K562	blood
18	chr12:49949200-49960400	Strong transcription	Fetal Stomach	stomach
19	chr12:49949400-49952600	Strong transcription	Fetal Muscle Trunk	muscle
20	chr12:49949400-49957000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:49949400-49957600	Strong transcription	Right Ventricle	heart
22	chr12:49949400-49958000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr12:49949400-49958200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr12:49949400-49958200	Strong transcription	Brain Anterior Caudate	brain
25	chr12:49949400-49958600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:49949400-49959000	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr12:49949400-49959200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr12:49949400-49959200	Strong transcription	Gastric	stomach
29	chr12:49949400-49959400	Strong transcription	Brain Germinal Matrix	brain
30	chr12:49949400-49959800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:49949400-49959800	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr12:49949400-49960000	Strong transcription	Thymus	Thymus
33	chr12:49949400-49960200	Strong transcription	NHLF	lung
34	chr12:49949600-49955600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:49949600-49956600	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr12:49949600-49958000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:49949600-49958000	Strong transcription	Fetal Muscle Leg	muscle
38	chr12:49949600-49958200	Strong transcription	Fetal Thymus	thymus
39	chr12:49949600-49958400	Strong transcription	Brain Cingulate Gyrus	brain
40	chr12:49949600-49959200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:49949600-49959600	Strong transcription	Placenta	Placenta
42	chr12:49949600-49959600	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr12:49949600-49959800	Strong transcription	Brain Hippocampus Middle	brain
44	chr12:49949600-49960000	Strong transcription	Fetal Intestine Large	intestine
45	chr12:49949600-49960400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr12:49949600-49960400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr12:49949800-49952600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr12:49949800-49954600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr12:49949800-49954600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:49949800-49957000	Strong transcription	Skeletal Muscle Female	skeletal muscle

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