Variant report

Variant	rs12041547
Chromosome Location	chr1:114316220-114316221
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114315143..114317661-chr1:114324442..114326870,2	MCF-7	breast:
2	chr1:114301076..114303485-chr1:114314228..114316888,3	MCF-7	breast:
3	chr1:114310854..114312625-chr1:114314961..114316732,2	MCF-7	breast:
4	chr1:114300225..114306650-chr1:114312596..114317597,9	K562	blood:

Variant related genes	Relation type
ENSG00000116793	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10858007	0.81[CHB][hapmap]
rs10858008	0.81[CHB][hapmap]
rs10858011	0.81[CHB][hapmap]
rs10858017	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10858018	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10858019	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10858021	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11102669	0.81[EUR][1000 genomes]
rs11102691	0.86[JPT][hapmap]
rs1113523	0.86[CHB][hapmap]
rs1146182	0.82[CEU][hapmap];0.85[CHB][hapmap];0.82[EUR][1000 genomes]
rs1146187	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs12044534	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12061482	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12063216	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1217192	0.81[CEU][hapmap]
rs1217193	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs1217200	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs1217201	0.81[CHB][hapmap]
rs1217210	0.82[EUR][1000 genomes]
rs1217211	0.82[CHB][hapmap]
rs1217226	0.81[CHB][hapmap]
rs1217227	0.81[CHB][hapmap]
rs1217228	0.81[CHB][hapmap]
rs1217234	0.81[CHB][hapmap]
rs1217376	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1217377	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1217380	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1217386	0.88[ASN][1000 genomes]
rs1217388	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1217389	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1217395	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1217396	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1217407	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1217410	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1217412	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1217413	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1217415	0.86[CHB][hapmap]
rs1217416	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1217421	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1230637	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1230638	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1230639	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1230640	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1230642	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1230645	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1230646	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1230647	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1230649	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1230655	0.82[EUR][1000 genomes]
rs1230656	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1230658	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs1230659	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs1230661	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1230671	0.82[EUR][1000 genomes]
rs1230678	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1230679	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1230683	0.82[EUR][1000 genomes]
rs1230685	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1230687	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1237682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12565589	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs12566340	0.81[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs1599971	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17031716	0.86[CHB][hapmap];0.80[EUR][1000 genomes]
rs1743605	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs1746853	0.82[CHB][hapmap]
rs1775754	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1777234	0.83[CEU][hapmap]
rs1777237	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs1777238	0.82[EUR][1000 genomes]
rs1777241	0.82[CEU][hapmap];0.81[CHB][hapmap];0.82[EUR][1000 genomes]
rs1935838	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1936398	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1981319	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2093436	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2243471	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2295853	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2358816	0.95[CEU][hapmap]
rs2359167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2488457	0.95[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2488458	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2636013	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2636014	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2797408	0.89[EUR][1000 genomes]
rs2797409	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2797412	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2798135	0.81[EUR][1000 genomes]
rs2798138	0.81[EUR][1000 genomes]
rs4145859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4423005	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4565712	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4600045	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4838997	0.82[EUR][1000 genomes]
rs4839335	0.84[EUR][1000 genomes]
rs61817589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6537792	0.83[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs6537795	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6663679	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6698586	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7526209	0.87[ASN][1000 genomes]
rs7529353	0.81[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs7553188	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9429730	0.81[CEU][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv831093	chr1:114254167-114378235	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114302600-114318000	Weak transcription	Spleen	Spleen
2	chr1:114302600-114321800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:114302800-114323200	Weak transcription	Aorta	Aorta
4	chr1:114302800-114323600	Weak transcription	Psoas Muscle	Psoas
5	chr1:114302800-114326000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:114302800-114326200	Weak transcription	Pancreas	Pancrea
7	chr1:114302800-114326200	Weak transcription	Right Ventricle	heart
8	chr1:114303000-114318800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr1:114303000-114319000	Weak transcription	Fetal Brain Male	brain
10	chr1:114303000-114319000	Weak transcription	HSMMtube	muscle
11	chr1:114303000-114323200	Weak transcription	Fetal Heart	heart
12	chr1:114303000-114326200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:114303200-114317200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:114303200-114328400	Weak transcription	A549	lung
15	chr1:114303400-114353800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:114304800-114320600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:114308200-114326600	Weak transcription	Colonic Mucosa	Colon
18	chr1:114309000-114323600	Weak transcription	Gastric	stomach
19	chr1:114309600-114353400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:114310200-114319000	Weak transcription	Left Ventricle	heart
21	chr1:114310600-114317200	Weak transcription	Fetal Brain Female	brain
22	chr1:114310600-114325400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:114310800-114318600	Weak transcription	HSMM	muscle
24	chr1:114310800-114319400	Weak transcription	NH-A	brain
25	chr1:114310800-114326000	Weak transcription	HMEC	breast
26	chr1:114311000-114316600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:114311000-114316600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr1:114311000-114316600	Weak transcription	Fetal Muscle Leg	muscle
29	chr1:114311000-114316600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:114311000-114316600	Weak transcription	Thymus	Thymus
31	chr1:114311000-114318400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:114311000-114318600	Weak transcription	Hela-S3	cervix
33	chr1:114311000-114319000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:114311000-114319000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:114311000-114319200	Weak transcription	Osteobl	bone
36	chr1:114311000-114323600	Weak transcription	Lung	lung
37	chr1:114311000-114324800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr1:114311000-114325800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr1:114311000-114326200	Weak transcription	HUVEC	blood vessel
40	chr1:114311000-114335600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:114311000-114336800	Weak transcription	Fetal Kidney	kidney
42	chr1:114311000-114341800	Weak transcription	Esophagus	oesophagus
43	chr1:114311200-114316600	Weak transcription	Liver	Liver
44	chr1:114311200-114317200	Weak transcription	Placenta	Placenta
45	chr1:114311200-114319000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:114311200-114325800	Weak transcription	NHEK	skin
47	chr1:114311400-114316600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr1:114311400-114317800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr1:114311400-114318000	Weak transcription	Primary B cells from peripheral blood	blood
50	chr1:114311400-114318400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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