Variant report

Variant	rs12139248
Chromosome Location	chr1:150108487-150108488
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150108071..150110117-chr1:150112375..150114316,2	MCF-7	breast:
2	chr1:150106267..150108980-chr1:150109547..150112029,2	K562	blood:
3	chr1:150087254..150089915-chr1:150106598..150108719,2	MCF-7	breast:

Extended variants
information (count: 125 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10494264	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10749674	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10888568	0.81[EUR][1000 genomes]
rs10888569	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10888572	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11205317	0.80[EUR][1000 genomes]
rs11205319	0.80[EUR][1000 genomes]
rs11205321	0.82[EUR][1000 genomes]
rs11205326	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11205329	0.85[EUR][1000 genomes]
rs11205331	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11205333	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11205337	0.80[AMR][1000 genomes]
rs11577346	0.86[EUR][1000 genomes]
rs11583720	0.88[EUR][1000 genomes]
rs11584091	0.89[EUR][1000 genomes]
rs11584354	0.85[EUR][1000 genomes]
rs11585955	0.88[EUR][1000 genomes]
rs11587963	0.89[EUR][1000 genomes]
rs11589585	0.80[EUR][1000 genomes]
rs11589922	0.84[EUR][1000 genomes]
rs11591200	0.84[EUR][1000 genomes]
rs12058090	0.80[EUR][1000 genomes]
rs12060027	0.81[EUR][1000 genomes]
rs12060211	0.80[EUR][1000 genomes]
rs12061167	0.80[EUR][1000 genomes]
rs12061196	0.80[EUR][1000 genomes]
rs12063059	0.80[EUR][1000 genomes]
rs12065681	0.80[EUR][1000 genomes]
rs12066132	0.80[EUR][1000 genomes]
rs12066293	0.80[EUR][1000 genomes]
rs12067422	0.80[EUR][1000 genomes]
rs12074281	0.82[EUR][1000 genomes]
rs12138231	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1339494	0.80[EUR][1000 genomes]
rs1339495	0.80[EUR][1000 genomes]
rs1382573	0.84[EUR][1000 genomes]
rs1545762	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1824849	0.84[EUR][1000 genomes]
rs1824850	0.84[EUR][1000 genomes]
rs1964542	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1975957	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2027349	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2039800	0.91[EUR][1000 genomes]
rs2169895	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2318763	0.88[EUR][1000 genomes]
rs28560140	0.80[EUR][1000 genomes]
rs28660389	0.81[EUR][1000 genomes]
rs28753817	0.80[EUR][1000 genomes]
rs3208509	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3850838	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3925724	0.91[EUR][1000 genomes]
rs4058847	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4926388	0.82[AFR][1000 genomes]
rs4926406	0.85[EUR][1000 genomes]
rs4926407	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4926408	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4926409	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4926412	0.82[AMR][1000 genomes]
rs55633125	0.80[EUR][1000 genomes]
rs55647342	0.83[EUR][1000 genomes]
rs55802315	0.80[EUR][1000 genomes]
rs55840680	0.89[EUR][1000 genomes]
rs55909733	0.89[EUR][1000 genomes]
rs55918911	0.81[EUR][1000 genomes]
rs56125600	0.81[EUR][1000 genomes]
rs56188926	0.88[EUR][1000 genomes]
rs56212907	0.87[EUR][1000 genomes]
rs56349882	0.84[EUR][1000 genomes]
rs56369603	0.89[EUR][1000 genomes]
rs57926929	0.85[EUR][1000 genomes]
rs58426216	0.87[EUR][1000 genomes]
rs59607464	0.84[EUR][1000 genomes]
rs6657062	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6666959	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6694729	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72692865	0.80[EUR][1000 genomes]
rs72692866	0.80[EUR][1000 genomes]
rs72692869	0.80[EUR][1000 genomes]
rs72692886	0.85[EUR][1000 genomes]
rs72692893	0.87[EUR][1000 genomes]
rs72692895	0.88[EUR][1000 genomes]
rs72692896	0.88[EUR][1000 genomes]
rs72692897	0.88[EUR][1000 genomes]
rs72692898	0.87[EUR][1000 genomes]
rs72692899	0.87[EUR][1000 genomes]
rs72692900	0.87[EUR][1000 genomes]
rs72692901	0.88[EUR][1000 genomes]
rs72694905	0.87[EUR][1000 genomes]
rs72694906	0.88[EUR][1000 genomes]
rs72694908	0.88[EUR][1000 genomes]
rs72694914	0.88[EUR][1000 genomes]
rs72694915	0.88[EUR][1000 genomes]
rs72694917	0.88[EUR][1000 genomes]
rs72694918	0.88[EUR][1000 genomes]
rs72694919	0.88[EUR][1000 genomes]
rs72694923	0.88[EUR][1000 genomes]
rs72694926	0.89[EUR][1000 genomes]
rs72694927	0.90[EUR][1000 genomes]
rs72694928	0.89[EUR][1000 genomes]
rs72694933	0.89[EUR][1000 genomes]
rs72694936	0.89[EUR][1000 genomes]
rs72694942	0.89[EUR][1000 genomes]
rs72694943	0.90[EUR][1000 genomes]
rs72694944	0.89[EUR][1000 genomes]
rs72694945	0.89[EUR][1000 genomes]
rs72694946	0.88[EUR][1000 genomes]
rs72694950	0.88[EUR][1000 genomes]
rs72694951	0.89[EUR][1000 genomes]
rs72694953	0.89[EUR][1000 genomes]
rs72694954	0.88[EUR][1000 genomes]
rs72694956	0.84[EUR][1000 genomes]
rs72694957	0.84[EUR][1000 genomes]
rs72694959	0.80[EUR][1000 genomes]
rs7519918	0.80[EUR][1000 genomes]
rs7520930	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7530922	0.80[EUR][1000 genomes]
rs7540847	0.82[EUR][1000 genomes]
rs7550323	0.82[EUR][1000 genomes]
rs7550350	0.80[EUR][1000 genomes]
rs7553622	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7554367	0.81[AFR][1000 genomes]
rs7555080	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9662055	0.80[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150040400-150121400	Weak transcription	Pancreas	Pancrea
2	chr1:150041000-150114400	Weak transcription	Right Ventricle	heart
3	chr1:150052000-150116800	Weak transcription	Spleen	Spleen
4	chr1:150055000-150120800	Weak transcription	Aorta	Aorta
5	chr1:150061000-150116800	Weak transcription	Ovary	ovary
6	chr1:150067000-150113200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:150067400-150121200	Weak transcription	Colonic Mucosa	Colon
8	chr1:150069000-150113800	Weak transcription	Fetal Kidney	kidney
9	chr1:150069000-150121000	Weak transcription	NHLF	lung
10	chr1:150071000-150121000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:150071200-150120600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:150072400-150121000	Weak transcription	Brain Angular Gyrus	brain
13	chr1:150077200-150113000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:150077400-150112800	Weak transcription	Fetal Heart	heart
15	chr1:150079200-150121000	Weak transcription	Thymus	Thymus
16	chr1:150083200-150116400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:150083600-150120800	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:150084000-150110600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:150085400-150116400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:150085400-150119000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:150085400-150120800	Weak transcription	NH-A	brain
22	chr1:150085400-150121200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:150085400-150121200	Weak transcription	Psoas Muscle	Psoas
24	chr1:150085600-150121200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:150085800-150121000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:150086800-150116400	Weak transcription	Left Ventricle	heart
27	chr1:150087000-150116400	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr1:150087000-150118400	Weak transcription	Fetal Intestine Large	intestine
29	chr1:150087000-150121200	Weak transcription	Esophagus	oesophagus
30	chr1:150087000-150121200	Weak transcription	Placenta	Placenta
31	chr1:150087400-150116800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:150087800-150110200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:150087800-150113800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:150087800-150118600	Weak transcription	Dnd41	blood
35	chr1:150087800-150120800	Weak transcription	Brain Anterior Caudate	brain
36	chr1:150087800-150121000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:150088000-150111400	Weak transcription	GM12878-XiMat	blood
38	chr1:150088000-150113800	Weak transcription	HSMMtube	muscle
39	chr1:150088000-150120800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:150088000-150120800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr1:150088800-150111000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:150091000-150116800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr1:150091200-150116600	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr1:150091200-150120400	Weak transcription	Colon Smooth Muscle	Colon
45	chr1:150091400-150119200	Weak transcription	Brain Germinal Matrix	brain
46	chr1:150091400-150121000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr1:150091600-150116600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:150091800-150116800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr1:150091800-150121000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:150094000-150110600	Weak transcription	NHDF-Ad	bronchial

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