Variant report

Variant	rs2124509
Chromosome Location	chr3:46994818-46994819
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46988617..46992704-chr3:46994196..46998366,6	K562	blood:
2	chr3:46993900..46995465-chr3:47020609..47023275,2	MCF-7	breast:
3	chr3:46994661..46997196-chr3:47000542..47003538,2	MCF-7	breast:
4	chr3:46993850..46995776-chr3:46997950..47000879,2	MCF-7	breast:
5	chr3:46992891..46995361-chr3:47004607..47007374,2	MCF-7	breast:
6	chr3:46993041..46995087-chr3:46996208..46998631,3	K562	blood:
7	chr3:46983607..46987334-chr3:46993451..46998407,5	K562	blood:

Variant related genes	Relation type
ENSG00000160796	Chromatin interaction
ENSG00000160799	Chromatin interaction

Extended variants
information (count: 156 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs10461017	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10461019	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10865945	1.00[EUR][1000 genomes]
rs11130108	0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11130109	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11706212	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11708257	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11709693	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11709876	0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11713537	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11922925	1.00[EUR][1000 genomes]
rs11928558	0.95[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12330516	1.00[EUR][1000 genomes]
rs12487763	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12488371	1.00[EUR][1000 genomes]
rs12631730	0.95[YRI][hapmap]
rs13062185	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13078181	1.00[EUR][1000 genomes]
rs13079416	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13082531	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13323092	0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs1378818	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1463394	0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466272	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466273	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466274	0.89[AMR][1000 genomes]
rs1473382	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1473384	1.00[EUR][1000 genomes]
rs1473385	1.00[EUR][1000 genomes]
rs1563431	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1563432	1.00[EUR][1000 genomes]
rs1814564	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1869870	0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1979736	1.00[EUR][1000 genomes]
rs2124510	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2350642	1.00[EUR][1000 genomes]
rs2385863	1.00[EUR][1000 genomes]
rs2385868	0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2385869	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28735306	1.00[EUR][1000 genomes]
rs2891887	1.00[AMR][1000 genomes]
rs2891893	0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs34147581	1.00[EUR][1000 genomes]
rs35366910	1.00[EUR][1000 genomes]
rs4018904	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs4282092	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4289375	0.87[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4324490	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4373094	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4378998	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4389512	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4450857	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4478107	0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4522803	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4525902	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4543047	0.91[YRI][hapmap];0.82[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	0.86[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682833	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682834	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4682835	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682836	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682838	0.88[YRI][hapmap];0.81[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	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682846	1.00[EUR][1000 genomes]
rs4682847	1.00[EUR][1000 genomes]
rs4683277	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683279	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683282	0.91[YRI][hapmap]
rs4683283	0.90[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683284	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683285	0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683286	0.87[YRI][hapmap];0.81[AFR][1000 genomes];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	0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683291	0.85[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683292	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	0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442042	0.84[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442043	0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442044	0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442047	0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442048	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442062	1.00[EUR][1000 genomes]
rs6442063	1.00[EUR][1000 genomes]
rs6766676	0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6767868	1.00[EUR][1000 genomes]
rs6768169	0.89[AMR][1000 genomes];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	0.85[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6804732	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6806521	0.90[YRI][hapmap];0.82[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	0.88[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831482	1.00[EUR][1000 genomes]
rs7615774	1.00[EUR][1000 genomes]
rs7621530	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7624549	0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7625011	0.91[YRI][hapmap];0.89[AMR][1000 genomes]
rs7630154	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs7630904	0.88[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7638549	1.00[YRI][hapmap];1.00[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	0.88[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7644382	0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs7646076	0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7649941	0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7650142	0.87[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652492	1.00[EUR][1000 genomes]
rs936173	1.00[EUR][1000 genomes]
rs936177	0.88[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936178	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936179	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936180	0.87[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936181	0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936182	0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936185	1.00[EUR][1000 genomes]
rs936186	0.96[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][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	0.85[YRI][hapmap];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:9 , 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	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	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
4	nsv460526	chr3:46935527-47001350	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv3800	chr3:46961648-47007241	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46977000-47000000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:46984200-46996400	Enhancers	Liver	Liver
3	chr3:46985600-46995200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:46985800-47004400	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr3:46988000-47003200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr3:46989200-46995400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:46989800-46995200	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr3:46989800-46998600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:46989800-47000600	Weak transcription	Brain Germinal Matrix	brain
10	chr3:46989800-47000600	Weak transcription	NHDF-Ad	bronchial
11	chr3:46989800-47001200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:46990000-46995400	Weak transcription	HSMMtube	muscle
13	chr3:46990000-47006800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:46990200-46995200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:46990200-46995400	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr3:46990200-46998200	Weak transcription	Aorta	Aorta
17	chr3:46990200-47000800	Weak transcription	Fetal Brain Female	brain
18	chr3:46990400-47000000	Enhancers	Primary T cells fromperipheralblood	blood
19	chr3:46991000-46995200	Weak transcription	NH-A	brain
20	chr3:46991000-46996800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:46991000-46998800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:46991000-47000200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:46991000-47001400	Weak transcription	Osteobl	bone
24	chr3:46991200-46995000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:46991200-46995200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:46991200-46995200	Weak transcription	HSMM	muscle
27	chr3:46991200-46997000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:46991200-46997800	Weak transcription	Brain Angular Gyrus	brain
29	chr3:46991200-46997800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:46991200-46998000	Weak transcription	Brain Substantia Nigra	brain
31	chr3:46991200-46998600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:46991200-46999600	Enhancers	A549	lung
33	chr3:46991200-47000000	Weak transcription	Fetal Lung	lung
34	chr3:46991200-47000200	Enhancers	Duodenum Mucosa	Duodenum
35	chr3:46991200-47000800	Weak transcription	Fetal Kidney	kidney
36	chr3:46991400-47000200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr3:46991400-47000400	Weak transcription	HMEC	breast
38	chr3:46991800-46995000	Weak transcription	Brain Hippocampus Middle	brain
39	chr3:46991800-46995200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr3:46991800-46997400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr3:46991800-46998600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:46992000-46995000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr3:46992000-46998000	Enhancers	Fetal Muscle Leg	muscle
44	chr3:46992000-47001400	Weak transcription	NHLF	lung
45	chr3:46992400-46998600	Weak transcription	Hela-S3	cervix
46	chr3:46992600-46995200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:46992600-46995400	Weak transcription	Placenta	Placenta
48	chr3:46992600-46995600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr3:46992600-46995600	Weak transcription	Gastric	stomach
50	chr3:46992600-46996600	Weak transcription	Brain Inferior Temporal Lobe	brain

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