Variant report

Variant	rs1180127
Chromosome Location	chr9:72903154-72903155
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 158 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:155)

rs_ID	r²[population]
rs10116549	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10117899	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125454	0.83[EUR][1000 genomes]
rs10126027	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10780870	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780871	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780924	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs10868742	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868800	1.00[CHB][hapmap]
rs10868807	0.86[AFR][1000 genomes]
rs10868808	0.89[YRI][hapmap]
rs1112937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11141917	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142348	1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11142354	0.86[AFR][1000 genomes]
rs11142356	0.86[AFR][1000 genomes]
rs11142363	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs11142365	0.95[EUR][1000 genomes]
rs11142367	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs11142368	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs11142370	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs11142371	0.90[AFR][1000 genomes]
rs11142373	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs11142374	0.88[AFR][1000 genomes]
rs11142375	0.88[ASN][1000 genomes]
rs11142377	1.00[CHB][hapmap]
rs11142379	0.93[CEU][hapmap];0.95[EUR][1000 genomes]
rs11142380	0.95[EUR][1000 genomes]
rs11142381	0.95[EUR][1000 genomes]
rs1180079	0.80[AFR][1000 genomes]
rs1180081	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1180083	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180087	0.86[AFR][1000 genomes]
rs1180088	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180089	1.00[CHB][hapmap]
rs1180091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180098	0.86[AFR][1000 genomes]
rs1180099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180100	1.00[CHB][hapmap]
rs1180101	0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs1180103	0.80[AFR][1000 genomes]
rs1180104	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1180106	0.86[AFR][1000 genomes]
rs1180107	0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs1180110	0.93[CEU][hapmap];0.97[EUR][1000 genomes]
rs1180111	0.97[EUR][1000 genomes]
rs1180112	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs1180114	0.88[AFR][1000 genomes]
rs1180115	0.81[AFR][1000 genomes]
rs1180117	0.95[YRI][hapmap];0.88[AFR][1000 genomes]
rs1180118	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1180120	0.88[AFR][1000 genomes]
rs1180122	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs1180124	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs1180125	0.86[AFR][1000 genomes]
rs1180126	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs1180128	0.94[AFR][1000 genomes]
rs1180132	0.88[AFR][1000 genomes]
rs1180133	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs11998951	0.95[YRI][hapmap];0.90[AFR][1000 genomes]
rs12005666	0.80[AFR][1000 genomes]
rs12006212	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs12115787	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12156606	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12349698	0.90[AMR][1000 genomes]
rs12377677	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12377766	0.80[AFR][1000 genomes]
rs12380844	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs17051515	0.80[ASN][1000 genomes]
rs17454349	0.80[ASN][1000 genomes]
rs17454433	0.80[ASN][1000 genomes]
rs17526808	0.80[ASN][1000 genomes]
rs1887451	0.83[EUR][1000 genomes]
rs1927096	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927100	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927101	0.80[ASN][1000 genomes]
rs1927118	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1927124	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927130	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927132	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927133	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927134	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927135	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927136	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1927144	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1927146	0.84[YRI][hapmap]
rs1986067	0.89[ASN][1000 genomes]
rs2026137	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs2148857	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148859	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148863	0.83[EUR][1000 genomes]
rs2148866	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2148867	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182734	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182737	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182738	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182741	1.00[ASN][1000 genomes]
rs2183362	0.84[AFR][1000 genomes]
rs2309634	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309645	1.00[CHB][hapmap]
rs2479033	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2768643	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2768644	0.80[AFR][1000 genomes]
rs2768645	0.85[AFR][1000 genomes]
rs2768646	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2773362	0.80[AFR][1000 genomes]
rs2773363	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773366	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2871293	0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs4384045	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4449855	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs4744591	0.84[AFR][1000 genomes]
rs4744989	0.92[AMR][1000 genomes]
rs4744993	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744999	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5019539	0.80[ASN][1000 genomes]
rs56059804	0.86[AFR][1000 genomes]
rs58720670	0.90[AFR][1000 genomes]
rs58881692	0.81[AFR][1000 genomes]
rs61531415	0.87[AFR][1000 genomes]
rs6560015	0.80[ASN][1000 genomes]
rs6560016	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6560018	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6560129	0.80[AFR][1000 genomes]
rs66524845	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs66658020	0.84[AFR][1000 genomes]
rs66756859	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs68171482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7019147	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020447	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024117	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024812	0.80[ASN][1000 genomes]
rs7034322	1.00[YRI][hapmap]
rs7043171	1.00[CHB][hapmap]
rs7047789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73454795	0.90[AFR][1000 genomes]
rs7852005	0.90[AFR][1000 genomes]
rs7853298	0.83[EUR][1000 genomes]
rs7858389	0.84[AFR][1000 genomes]
rs7858907	0.80[AFR][1000 genomes]
rs7858988	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs7860729	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7867727	0.86[AFR][1000 genomes]
rs7868564	0.84[AFR][1000 genomes]
rs7869429	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871674	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs943534	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943535	1.00[CHB][hapmap]
rs943536	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs943540	0.80[YRI][hapmap]

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	nsv1047862	chr9:72746875-73138287	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv831615	chr9:72852705-73019692	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1049132	chr9:72895382-73005897	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72875000-72949800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:72875400-72906200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:72876000-72906200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:72876400-72916800	Weak transcription	Colonic Mucosa	Colon
5	chr9:72876400-72939400	Weak transcription	Spleen	Spleen
6	chr9:72876400-72942600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr9:72876400-72955200	Weak transcription	Stomach Mucosa	stomach
8	chr9:72877000-72904800	Weak transcription	Brain Germinal Matrix	brain
9	chr9:72877000-72939800	Weak transcription	Gastric	stomach
10	chr9:72877000-72942800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:72877600-72909600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr9:72877600-72935800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:72878600-72937600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr9:72880000-72939400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr9:72880200-72906200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr9:72881000-72905000	Weak transcription	Brain Hippocampus Middle	brain
17	chr9:72881000-72905000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr9:72882800-72906000	Weak transcription	K562	blood
19	chr9:72885400-72916800	Weak transcription	Esophagus	oesophagus
20	chr9:72887600-72906200	Weak transcription	Psoas Muscle	Psoas
21	chr9:72887600-72916800	Weak transcription	Aorta	Aorta
22	chr9:72889400-72904200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr9:72890000-72905800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:72890400-72904800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:72891000-72905000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr9:72891000-72908800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr9:72891000-72911000	Strong transcription	HSMM	muscle
28	chr9:72891000-72923400	Strong transcription	Dnd41	blood
29	chr9:72891200-72907400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr9:72891400-72948200	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr9:72891600-72905200	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr9:72892800-72907600	Strong transcription	NH-A	brain
33	chr9:72893000-72904000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:72893000-72904000	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr9:72893000-72906600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr9:72893200-72903200	Strong transcription	Adipose Nuclei	Adipose
37	chr9:72893400-72904200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr9:72893400-72906000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr9:72893400-72907400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr9:72893400-72908000	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr9:72894600-72917000	Weak transcription	Pancreas	Pancrea
42	chr9:72895400-72903800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr9:72895400-72906600	Weak transcription	Fetal Brain Female	brain
44	chr9:72896200-72906200	Weak transcription	Brain Anterior Caudate	brain
45	chr9:72896200-72916800	Weak transcription	Right Ventricle	heart
46	chr9:72897800-72905000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr9:72897800-72912800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr9:72898200-72906200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr9:72898200-72922200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr9:72898600-72906200	Weak transcription	Fetal Intestine Small	intestine

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