Variant report

Variant	rs10125454
Chromosome Location	chr9:72767405-72767406
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 133 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10114223	0.83[AFR][1000 genomes]
rs10116027	0.90[AFR][1000 genomes]
rs10116549	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10117899	0.87[EUR][1000 genomes]
rs10126027	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1012992	0.84[AFR][1000 genomes]
rs1012993	0.84[AFR][1000 genomes]
rs10521437	0.85[ASN][1000 genomes]
rs10746819	0.84[AFR][1000 genomes]
rs10780851	0.85[AFR][1000 genomes]
rs10780866	0.88[AFR][1000 genomes]
rs10780869	0.82[AFR][1000 genomes]
rs10780870	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10780871	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10868742	0.87[EUR][1000 genomes]
rs10868808	0.81[YRI][hapmap]
rs1112937	1.00[CEU][hapmap];0.89[YRI][hapmap];0.80[EUR][1000 genomes]
rs11141917	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11142348	0.88[YRI][hapmap]
rs11142363	0.87[YRI][hapmap]
rs11142367	0.91[YRI][hapmap]
rs11142368	0.92[YRI][hapmap]
rs11142370	0.88[YRI][hapmap]
rs11142373	0.87[YRI][hapmap]
rs1180081	0.83[EUR][1000 genomes]
rs1180082	1.00[CEU][hapmap];0.91[YRI][hapmap]
rs1180083	0.82[EUR][1000 genomes]
rs1180086	1.00[CEU][hapmap];0.92[YRI][hapmap];0.82[EUR][1000 genomes]
rs1180088	0.82[EUR][1000 genomes]
rs1180091	1.00[CEU][hapmap];0.88[YRI][hapmap];0.83[EUR][1000 genomes]
rs1180094	1.00[CEU][hapmap];0.92[YRI][hapmap];0.83[EUR][1000 genomes]
rs1180099	1.00[CEU][hapmap];0.87[YRI][hapmap];0.83[EUR][1000 genomes]
rs1180101	0.88[YRI][hapmap]
rs1180102	0.80[YRI][hapmap]
rs1180104	0.92[YRI][hapmap]
rs1180107	0.88[YRI][hapmap]
rs1180110	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs1180111	0.80[EUR][1000 genomes]
rs1180112	0.92[YRI][hapmap]
rs1180117	0.87[YRI][hapmap]
rs1180118	0.92[YRI][hapmap]
rs1180122	0.88[YRI][hapmap]
rs1180124	0.87[YRI][hapmap]
rs1180126	0.92[YRI][hapmap]
rs1180127	1.00[CEU][hapmap];0.92[YRI][hapmap];0.83[EUR][1000 genomes]
rs1180133	0.88[YRI][hapmap]
rs11998951	0.87[YRI][hapmap]
rs12006212	0.87[YRI][hapmap]
rs12156606	0.92[YRI][hapmap]
rs12236327	0.82[AFR][1000 genomes]
rs12377677	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12380844	0.91[YRI][hapmap]
rs17051515	0.90[ASN][1000 genomes]
rs17453310	1.00[ASN][1000 genomes]
rs17454349	0.90[ASN][1000 genomes]
rs17454433	0.90[ASN][1000 genomes]
rs17526808	0.90[ASN][1000 genomes]
rs1887451	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1887452	0.80[AFR][1000 genomes]
rs1927096	0.84[EUR][1000 genomes]
rs1927100	0.87[EUR][1000 genomes]
rs1927101	0.90[ASN][1000 genomes]
rs1927113	1.00[ASN][1000 genomes]
rs1927118	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1927120	0.84[AFR][1000 genomes]
rs1927121	0.86[AFR][1000 genomes]
rs1927122	0.90[AFR][1000 genomes]
rs1927124	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1927125	0.80[AFR][1000 genomes]
rs1927126	0.86[AFR][1000 genomes]
rs1927127	0.86[AFR][1000 genomes]
rs1927130	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1927132	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1927133	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1927134	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1927135	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1927136	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1927140	0.83[AFR][1000 genomes]
rs1927144	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1986067	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2026137	0.92[YRI][hapmap]
rs2148857	0.84[EUR][1000 genomes]
rs2148859	0.82[EUR][1000 genomes]
rs2148863	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148866	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2148867	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2148868	0.81[AFR][1000 genomes]
rs2182734	0.84[EUR][1000 genomes]
rs2182735	1.00[CEU][hapmap];0.91[YRI][hapmap];0.84[EUR][1000 genomes]
rs2182737	0.84[EUR][1000 genomes]
rs2182738	0.82[EUR][1000 genomes]
rs2182740	0.84[AFR][1000 genomes]
rs2182741	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2209781	0.81[AFR][1000 genomes]
rs2309632	0.82[AFR][1000 genomes]
rs2309634	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2309644	1.00[CEU][hapmap];0.92[YRI][hapmap];0.84[EUR][1000 genomes]
rs2479033	0.84[EUR][1000 genomes]
rs2768643	0.83[EUR][1000 genomes]
rs2768646	0.84[EUR][1000 genomes]
rs2773363	0.84[EUR][1000 genomes]
rs2773366	0.84[EUR][1000 genomes]
rs2871293	0.88[YRI][hapmap]
rs2871296	0.80[AFR][1000 genomes]
rs4322072	0.80[AFR][1000 genomes]
rs4449855	0.87[YRI][hapmap]
rs4531114	0.86[AFR][1000 genomes]
rs4744984	0.85[AFR][1000 genomes]
rs4744993	0.87[EUR][1000 genomes]
rs4744994	0.85[YRI][hapmap]
rs4744999	0.83[EUR][1000 genomes]
rs5019539	0.90[ASN][1000 genomes]
rs6560015	0.90[ASN][1000 genomes]
rs6560016	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6560018	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs68171482	0.83[EUR][1000 genomes]
rs7019147	0.87[EUR][1000 genomes]
rs7020447	0.83[EUR][1000 genomes]
rs7024117	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7024812	0.90[ASN][1000 genomes]
rs7034322	0.92[YRI][hapmap]
rs7043789	0.81[ASN][1000 genomes]
rs7047789	1.00[CEU][hapmap];0.92[YRI][hapmap];0.80[EUR][1000 genomes]
rs73647464	0.81[ASN][1000 genomes]
rs7846908	0.81[ASN][1000 genomes]
rs7853298	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7856528	0.84[AFR][1000 genomes]
rs7857292	0.80[AFR][1000 genomes]
rs7858988	0.87[YRI][hapmap]
rs7860729	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7869429	0.87[EUR][1000 genomes]
rs943536	0.87[YRI][hapmap]

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	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

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72726800-72785200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr9:72727000-72776200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:72731200-72768400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:72741600-72775400	Weak transcription	Adipose Nuclei	Adipose
5	chr9:72741600-72789400	Weak transcription	Spleen	Spleen
6	chr9:72750400-72771600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr9:72751000-72771800	Weak transcription	Aorta	Aorta
8	chr9:72752000-72779600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:72752400-72775200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr9:72752600-72771400	Weak transcription	NH-A	brain
11	chr9:72753800-72770000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr9:72758800-72772200	Weak transcription	Colonic Mucosa	Colon
13	chr9:72759200-72774400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:72759600-72800000	Weak transcription	Right Ventricle	heart
15	chr9:72759800-72774000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr9:72759800-72792200	Weak transcription	HMEC	breast
17	chr9:72760000-72768600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:72760000-72785200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:72761200-72768400	Weak transcription	HSMM	muscle
20	chr9:72762800-72770000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr9:72763200-72769800	Weak transcription	Psoas Muscle	Psoas
22	chr9:72763400-72770800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr9:72766000-72767800	Genic enhancers	Colon Smooth Muscle	Colon
24	chr9:72766000-72767800	Enhancers	Stomach Smooth Muscle	stomach
25	chr9:72766000-72768400	Enhancers	Rectal Smooth Muscle	rectum
26	chr9:72766200-72769200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:72766200-72785200	Weak transcription	Left Ventricle	heart
28	chr9:72766400-72767800	Enhancers	H9 Cell Line	embryonic stem cell
29	chr9:72766400-72767800	Enhancers	Fetal Stomach	stomach
30	chr9:72766400-72768200	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr9:72766400-72768400	Enhancers	H1 Cell Line	embryonic stem cell
32	chr9:72766600-72767600	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr9:72766600-72768600	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr9:72766800-72767600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr9:72766800-72768400	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr9:72767000-72769000	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr9:72767000-72770000	Weak transcription	Ovary	ovary
38	chr9:72767000-72770400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr9:72767000-72775400	Weak transcription	Right Atrium	heart
40	chr9:72767200-72768400	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr9:72767400-72769400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr9:72767400-72769800	Weak transcription	HSMMtube	muscle
43	chr9:72767400-72780200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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