Variant report

Variant	rs4389512
Chromosome Location	chr3:47012179-47012180
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46992711..46994503-chr3:47010548..47012316,2	K562	blood:
2	chr3:47007836..47011318-chr3:47011441..47014509,4	MCF-7	breast:
3	chr3:46995234..46997010-chr3:47011388..47013253,2	K562	blood:
4	chr3:47001947..47004283-chr3:47011185..47013637,2	MCF-7	breast:
5	chr3:47011340..47013025-chr3:47015501..47017285,2	MCF-7	breast:

Extended variants
information (count: 165 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:157)

rs_ID	r²[population]
rs10461017	0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10461019	0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10865945	1.00[EUR][1000 genomes]
rs11130108	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11130109	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11706212	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11708257	0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11709693	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11709876	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11713537	0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11922925	1.00[EUR][1000 genomes]
rs11928558	0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12330516	1.00[EUR][1000 genomes]
rs12487763	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12488371	1.00[EUR][1000 genomes]
rs12631730	0.86[YRI][hapmap]
rs13062185	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13062516	0.94[AFR][1000 genomes]
rs13074884	0.82[AFR][1000 genomes]
rs13078181	1.00[EUR][1000 genomes]
rs13079416	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13082531	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13323092	0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs1378818	0.92[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1463394	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466272	0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466273	0.83[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466274	0.83[YRI][hapmap];0.89[AMR][1000 genomes]
rs1473382	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1473384	1.00[EUR][1000 genomes]
rs1473385	1.00[EUR][1000 genomes]
rs1563431	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1563432	1.00[EUR][1000 genomes]
rs1814564	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1869870	0.86[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1874264	1.00[EUR][1000 genomes]
rs1979736	1.00[EUR][1000 genomes]
rs2124509	0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2124510	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2350642	1.00[EUR][1000 genomes]
rs2385863	1.00[EUR][1000 genomes]
rs2385868	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2385869	0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2385872	0.83[AFR][1000 genomes]
rs28735306	1.00[EUR][1000 genomes]
rs2891887	1.00[AMR][1000 genomes]
rs2891893	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs34147581	1.00[EUR][1000 genomes]
rs35366910	1.00[EUR][1000 genomes]
rs4018904	0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs4282092	0.91[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4289375	0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4324490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4373094	0.92[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4378998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4435676	0.81[AFR][1000 genomes]
rs4450857	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4478107	0.86[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4522803	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4525902	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4543047	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682828	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682832	0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682833	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682834	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4682835	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682836	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682838	0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682840	0.89[AMR][1000 genomes]
rs4682841	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682843	0.83[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682846	1.00[EUR][1000 genomes]
rs4682847	1.00[EUR][1000 genomes]
rs4683277	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683279	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683282	1.00[YRI][hapmap]
rs4683283	0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683284	0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683285	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683286	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683288	1.00[EUR][1000 genomes]
rs4683289	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683290	0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683291	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683292	0.86[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683293	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683303	1.00[EUR][1000 genomes]
rs6442041	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442042	0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442043	0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442044	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442047	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442048	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442050	0.86[AFR][1000 genomes]
rs6442062	1.00[EUR][1000 genomes]
rs6442063	1.00[EUR][1000 genomes]
rs6766676	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6767868	1.00[EUR][1000 genomes]
rs6768169	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6772449	1.00[EUR][1000 genomes]
rs6775797	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6780994	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6785462	0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6804732	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6806521	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808052	1.00[EUR][1000 genomes]
rs6808117	1.00[EUR][1000 genomes]
rs6808629	1.00[EUR][1000 genomes]
rs6809904	0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831482	1.00[EUR][1000 genomes]
rs7615774	1.00[EUR][1000 genomes]
rs7621530	0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7624549	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7625011	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7627241	0.81[AFR][1000 genomes]
rs7630154	0.87[YRI][hapmap];1.00[EUR][1000 genomes]
rs7630904	0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7638549	0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7641494	1.00[EUR][1000 genomes]
rs7643150	1.00[EUR][1000 genomes]
rs7643868	0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7644382	0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs7646076	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7649413	1.00[EUR][1000 genomes]
rs7649941	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7650142	0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652492	1.00[EUR][1000 genomes]
rs936173	1.00[EUR][1000 genomes]
rs936177	0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936178	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936179	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936180	0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936181	0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936182	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936185	1.00[EUR][1000 genomes]
rs936186	0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9637426	0.82[AFR][1000 genomes]
rs9810881	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9812407	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9819344	1.00[EUR][1000 genomes]
rs9819475	1.00[EUR][1000 genomes]
rs9823480	1.00[EUR][1000 genomes]
rs9826488	1.00[EUR][1000 genomes]
rs9827293	1.00[EUR][1000 genomes]
rs9828473	1.00[EUR][1000 genomes]
rs9833500	1.00[EUR][1000 genomes]
rs9836801	1.00[EUR][1000 genomes]
rs9850151	1.00[EUR][1000 genomes]
rs9852167	1.00[EUR][1000 genomes]
rs9861247	1.00[EUR][1000 genomes]
rs9861265	1.00[EUR][1000 genomes]
rs9862711	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9869489	1.00[EUR][1000 genomes]
rs9878813	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9883152	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9883909	1.00[EUR][1000 genomes]
rs9990284	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1012682	chr3:46973552-47016357	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv1009396	chr3:46994991-47048166	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47002400-47013200	Weak transcription	NH-A	brain
2	chr3:47003200-47015800	Weak transcription	Fetal Brain Male	brain
3	chr3:47003200-47016800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:47004800-47012600	Weak transcription	HSMM	muscle
5	chr3:47004800-47017200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:47004800-47017200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:47006400-47012600	Genic enhancers	Primary B cells from peripheral blood	blood
8	chr3:47006400-47013000	Genic enhancers	K562	blood
9	chr3:47006400-47013200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:47006400-47013600	Genic enhancers	Fetal Intestine Small	intestine
11	chr3:47006600-47013200	Strong transcription	Dnd41	blood
12	chr3:47006600-47013400	Genic enhancers	Primary T cells fromperipheralblood	blood
13	chr3:47006600-47014400	Genic enhancers	Fetal Thymus	thymus
14	chr3:47006600-47017000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr3:47006800-47012600	Genic enhancers	Primary B cells from cord blood	blood
16	chr3:47006800-47013200	Genic enhancers	Esophagus	oesophagus
17	chr3:47006800-47013600	Genic enhancers	Lung	lung
18	chr3:47006800-47014600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:47007000-47017400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:47007200-47013800	Enhancers	Fetal Heart	heart
21	chr3:47007200-47017400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:47007400-47012400	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr3:47007400-47012800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:47007400-47012800	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr3:47007400-47013800	Strong transcription	Fetal Stomach	stomach
26	chr3:47007600-47012200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr3:47007600-47012400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:47007600-47012600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:47007600-47012800	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr3:47007600-47013800	Enhancers	Pancreas	Pancrea
31	chr3:47007600-47014600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr3:47007600-47014800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:47007600-47016200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr3:47007600-47017200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:47007600-47017200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:47007600-47017400	Weak transcription	HSMMtube	muscle
37	chr3:47007800-47012600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr3:47007800-47013600	Enhancers	Adipose Nuclei	Adipose
39	chr3:47008000-47013400	Enhancers	Right Ventricle	heart
40	chr3:47008200-47013400	Enhancers	Ovary	ovary
41	chr3:47008200-47013400	Enhancers	Right Atrium	heart
42	chr3:47008200-47014600	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr3:47008400-47013000	Genic enhancers	Primary monocytes fromperipheralblood	blood
44	chr3:47008400-47015600	Weak transcription	Hela-S3	cervix
45	chr3:47008600-47012400	Genic enhancers	Monocytes-CD14+_RO01746	blood
46	chr3:47008600-47013600	Enhancers	Brain Hippocampus Middle	brain
47	chr3:47009000-47012600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:47009200-47017200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr3:47009400-47014800	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr3:47009600-47012400	Genic enhancers	Duodenum Mucosa	Duodenum

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