Variant report

Variant	rs4682834
Chromosome Location	chr3:46999909-46999910
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46988825..46991481-chr3:46997444..47000413,2	MCF-7	breast:
2	chr3:46997668..47000138-chr3:47008778..47011598,2	MCF-7	breast:
3	chr3:46993850..46995776-chr3:46997950..47000879,2	MCF-7	breast:
4	chr3:46987457..46990723-chr3:46999774..47002993,3	MCF-7	breast:

Extended variants
information (count: 159 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:149)

rs_ID	r²[population]
rs10461017	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10461019	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10865945	1.00[EUR][1000 genomes]
rs11130108	1.00[EUR][1000 genomes]
rs11130109	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11706212	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11708257	1.00[EUR][1000 genomes]
rs11709693	1.00[EUR][1000 genomes]
rs11709876	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11713537	1.00[EUR][1000 genomes]
rs11922925	1.00[EUR][1000 genomes]
rs11928558	1.00[EUR][1000 genomes]
rs12330516	1.00[EUR][1000 genomes]
rs12487763	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12488371	1.00[EUR][1000 genomes]
rs13062185	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13062516	0.82[AFR][1000 genomes]
rs13074884	0.80[AFR][1000 genomes]
rs13078181	1.00[EUR][1000 genomes]
rs13079416	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13082531	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13323092	1.00[EUR][1000 genomes]
rs1378818	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1463394	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1466272	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1466273	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1466274	0.86[AFR][1000 genomes]
rs1473382	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1473384	1.00[EUR][1000 genomes]
rs1473385	1.00[EUR][1000 genomes]
rs1563431	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1563432	1.00[EUR][1000 genomes]
rs1814564	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1869870	1.00[EUR][1000 genomes]
rs1874264	1.00[EUR][1000 genomes]
rs1979736	1.00[EUR][1000 genomes]
rs2124509	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2124510	0.87[AFR][1000 genomes]
rs2350642	1.00[EUR][1000 genomes]
rs2385863	1.00[EUR][1000 genomes]
rs2385868	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2385869	0.81[AFR][1000 genomes]
rs2385872	0.86[AFR][1000 genomes]
rs28735306	1.00[EUR][1000 genomes]
rs2891893	0.93[AFR][1000 genomes]
rs34147581	1.00[EUR][1000 genomes]
rs35366910	1.00[EUR][1000 genomes]
rs4018904	1.00[EUR][1000 genomes]
rs4282092	1.00[EUR][1000 genomes]
rs4289375	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4324490	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4373094	1.00[EUR][1000 genomes]
rs4378998	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4389512	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4450857	1.00[EUR][1000 genomes]
rs4478107	1.00[EUR][1000 genomes]
rs4522803	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4525902	1.00[EUR][1000 genomes]
rs4543047	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4682828	1.00[EUR][1000 genomes]
rs4682832	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4682833	1.00[EUR][1000 genomes]
rs4682835	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4682836	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4682838	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4682841	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4682843	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4682846	1.00[EUR][1000 genomes]
rs4682847	1.00[EUR][1000 genomes]
rs4683277	1.00[EUR][1000 genomes]
rs4683279	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4683283	1.00[EUR][1000 genomes]
rs4683284	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4683285	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4683286	1.00[EUR][1000 genomes]
rs4683288	1.00[EUR][1000 genomes]
rs4683289	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4683290	1.00[EUR][1000 genomes]
rs4683291	1.00[EUR][1000 genomes]
rs4683292	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4683293	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4683303	1.00[EUR][1000 genomes]
rs6442041	1.00[EUR][1000 genomes]
rs6442042	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6442043	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6442044	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6442047	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6442048	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6442062	1.00[EUR][1000 genomes]
rs6442063	1.00[EUR][1000 genomes]
rs6766676	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6767868	1.00[EUR][1000 genomes]
rs6768169	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6775797	1.00[EUR][1000 genomes]
rs6780994	1.00[EUR][1000 genomes]
rs6785462	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6804732	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6806521	0.88[AFR][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	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831482	1.00[EUR][1000 genomes]
rs7615774	1.00[EUR][1000 genomes]
rs7621530	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7624549	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7625011	0.81[AFR][1000 genomes]
rs7630154	1.00[EUR][1000 genomes]
rs7630904	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7631423	0.81[AFR][1000 genomes]
rs7638549	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7641494	1.00[EUR][1000 genomes]
rs7643150	1.00[EUR][1000 genomes]
rs7643868	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7644382	1.00[EUR][1000 genomes]
rs7646076	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7649941	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7650142	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7652492	1.00[EUR][1000 genomes]
rs936173	1.00[EUR][1000 genomes]
rs936177	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs936178	1.00[EUR][1000 genomes]
rs936179	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs936180	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs936181	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs936182	1.00[EUR][1000 genomes]
rs936185	1.00[EUR][1000 genomes]
rs936186	1.00[EUR][1000 genomes]
rs9637426	0.82[AFR][1000 genomes]
rs9810881	1.00[EUR][1000 genomes]
rs9812407	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	1.00[EUR][1000 genomes]
rs9869489	1.00[EUR][1000 genomes]
rs9878813	1.00[EUR][1000 genomes]
rs9883152	1.00[EUR][1000 genomes]
rs9883909	1.00[EUR][1000 genomes]
rs9990284	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	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

No data

Chromatin state (count:123 , 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	chr3:46985800-47004400	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr3:46988000-47003200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr3:46989800-47000600	Weak transcription	Brain Germinal Matrix	brain
5	chr3:46989800-47000600	Weak transcription	NHDF-Ad	bronchial
6	chr3:46989800-47001200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:46990000-47006800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:46990200-47000800	Weak transcription	Fetal Brain Female	brain
9	chr3:46990400-47000000	Enhancers	Primary T cells fromperipheralblood	blood
10	chr3:46991000-47000200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:46991000-47001400	Weak transcription	Osteobl	bone
12	chr3:46991200-47000000	Weak transcription	Fetal Lung	lung
13	chr3:46991200-47000200	Enhancers	Duodenum Mucosa	Duodenum
14	chr3:46991200-47000800	Weak transcription	Fetal Kidney	kidney
15	chr3:46991400-47000200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:46991400-47000400	Weak transcription	HMEC	breast
17	chr3:46992000-47001400	Weak transcription	NHLF	lung
18	chr3:46993400-47003600	Enhancers	Fetal Heart	heart
19	chr3:46993600-47000000	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr3:46993600-47003200	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr3:46994200-47001200	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr3:46994200-47001600	Enhancers	Colon Smooth Muscle	Colon
23	chr3:46994200-47002200	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr3:46994200-47003200	Genic enhancers	Fetal Intestine Small	intestine
25	chr3:46994800-47001600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:46995000-47001600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:46995400-47002200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr3:46995400-47003200	Enhancers	Fetal Intestine Large	intestine
29	chr3:46995400-47003400	Enhancers	Primary hematopoietic stem cells	blood
30	chr3:46995600-47000400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr3:46995600-47004200	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr3:46995800-47000200	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr3:46995800-47000200	Weak transcription	HUVEC	blood vessel
34	chr3:46995800-47001400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:46995800-47001400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:46995800-47002400	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr3:46995800-47003200	Enhancers	Primary B cells from cord blood	blood
38	chr3:46995800-47005200	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr3:46996000-47000800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:46996000-47001400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr3:46996000-47001400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:46996000-47001600	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:46996000-47004200	Enhancers	Primary T cells from cord blood	blood
44	chr3:46996000-47004600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr3:46996000-47004800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr3:46996000-47007200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:46996400-47000600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr3:46996400-47005000	Genic enhancers	Primary B cells from peripheral blood	blood
49	chr3:46996600-47001600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:46996600-47002600	Enhancers	Rectal Mucosa Donor 31	rectum

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