Variant report

Variant	rs12551818
Chromosome Location	chr9:100144043-100144044
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:100135058..100137231-chr9:100142276..100144723,2	MCF-7	breast:

Extended variants
information (count: 120 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1048451	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10521029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs10817384	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10817491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10817504	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10981297	0.94[CEU][hapmap]
rs10981367	1.00[CEU][hapmap];0.85[YRI][hapmap]
rs10981434	0.82[EUR][1000 genomes]
rs10981444	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10981460	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10981688	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10981701	0.88[AMR][1000 genomes]
rs10981784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10981800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10981801	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1123379	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11581	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12115447	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12115448	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12377538	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12378350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12550923	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs12551740	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12552101	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12552659	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12553155	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12553213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12553259	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12554363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12555277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13285567	0.93[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13286510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13287082	0.94[CEU][hapmap]
rs13289134	0.94[CEU][hapmap]
rs13289813	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13292715	0.82[EUR][1000 genomes]
rs13300328	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13301045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13301965	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1531440	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1564048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1564050	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16919506	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16919656	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16919661	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16919671	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16919675	0.95[CEU][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1986462	0.89[CEU][hapmap]
rs2045729	1.00[CEU][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2045730	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2045731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279113	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2290933	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2306090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2306092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2306094	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2401384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34135027	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34183765	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34355647	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34476799	0.82[EUR][1000 genomes]
rs34564795	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34609282	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34616426	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34754033	0.86[EUR][1000 genomes]
rs34870571	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34905303	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34954690	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35066943	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35123877	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35534888	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35623544	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35737497	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35778461	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35778718	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35788892	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3747490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3747491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3747492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3747495	1.00[CEU][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3747498	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3747499	1.00[CEU][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3747504	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3747506	0.94[CEU][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3747507	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3747510	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747511	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3827484	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827485	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3994560	1.00[CEU][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4128763	1.00[CEU][hapmap]
rs41316960	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4742686	0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743069	0.85[EUR][1000 genomes]
rs4743070	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs4743073	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4743082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743086	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60681062	0.86[EUR][1000 genomes]
rs62557460	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62557461	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62557462	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62557463	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62559861	0.83[EUR][1000 genomes]
rs6478038	0.84[EUR][1000 genomes]
rs6478039	0.84[EUR][1000 genomes]
rs7020530	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7038496	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7041222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73565808	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7859665	0.82[JPT][hapmap]
rs7872669	0.85[EUR][1000 genomes]
rs7874652	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs898869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs898870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9696058	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][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	nsv1036105	chr9:100131266-100171816	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100091600-100149200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr9:100108000-100148200	Weak transcription	Esophagus	oesophagus
3	chr9:100115400-100144600	Weak transcription	Hela-S3	cervix
4	chr9:100117400-100145000	Weak transcription	Colon Smooth Muscle	Colon
5	chr9:100117600-100146400	Weak transcription	Small Intestine	intestine
6	chr9:100126600-100148400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:100127000-100148600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr9:100129000-100144400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr9:100132000-100149000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:100132400-100146800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr9:100132600-100144400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:100132600-100146800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:100132600-100148600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr9:100132600-100149400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr9:100132600-100149400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:100133400-100148400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:100134000-100144400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:100134600-100148600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:100136600-100148000	Weak transcription	Colonic Mucosa	Colon
20	chr9:100138600-100146000	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr9:100139400-100145000	Weak transcription	Gastric	stomach
22	chr9:100139400-100146200	Weak transcription	Aorta	Aorta
23	chr9:100139400-100148400	Weak transcription	Pancreas	Pancrea
24	chr9:100139400-100148800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr9:100139400-100149400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr9:100139800-100149400	Weak transcription	Brain Substantia Nigra	brain
27	chr9:100140000-100145000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr9:100140000-100145400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr9:100140000-100146000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr9:100140000-100146600	Weak transcription	Spleen	Spleen
31	chr9:100140000-100149200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr9:100140000-100149400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr9:100140000-100149400	Weak transcription	Brain Angular Gyrus	brain
34	chr9:100140000-100149400	Weak transcription	Ovary	ovary
35	chr9:100140000-100149400	Weak transcription	Right Ventricle	heart
36	chr9:100140200-100149400	Weak transcription	Brain Germinal Matrix	brain
37	chr9:100140800-100145600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr9:100141000-100144400	Weak transcription	Fetal Brain Male	brain
39	chr9:100141000-100145000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr9:100141000-100146000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr9:100141000-100146200	Weak transcription	Brain Anterior Caudate	brain
42	chr9:100141000-100147000	Weak transcription	Adipose Nuclei	Adipose
43	chr9:100141200-100145000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr9:100141200-100146200	Weak transcription	Fetal Stomach	stomach
45	chr9:100141200-100147400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr9:100141200-100149000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr9:100141200-100149400	Weak transcription	Left Ventricle	heart
48	chr9:100141200-100150800	Weak transcription	Lung	lung
49	chr9:100141400-100146400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr9:100141400-100147400	Weak transcription	Brain Hippocampus Middle	brain

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