Variant report

Variant	rs4525902
Chromosome Location	chr3:47003972-47003973
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46988088..46989870-chr3:47001912..47004802,2	MCF-7	breast:
2	chr3:47000539..47004616-chr3:47005854..47010349,8	K562	blood:
3	chr3:47000442..47004800-chr3:47015859..47022252,7	K562	blood:
4	chr3:47001947..47004283-chr3:47011185..47013637,2	MCF-7	breast:
5	chr3:47000243..47004408-chr3:47018008..47023852,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160799	Chromatin interaction
ENSG00000160796	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs10461017	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10461019	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10865945	1.00[EUR][1000 genomes]
rs11130108	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11130109	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11706212	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11708257	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11709693	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11709876	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11713537	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11922925	1.00[EUR][1000 genomes]
rs11928558	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]
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	1.00[EUR][1000 genomes]
rs1378818	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1463394	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	0.89[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	0.80[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	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2124510	1.00[AMR][1000 genomes]
rs2350642	1.00[EUR][1000 genomes]
rs2385863	1.00[EUR][1000 genomes]
rs2385868	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2385869	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28735306	1.00[EUR][1000 genomes]
rs2891887	1.00[AMR][1000 genomes]
rs2891893	0.89[AMR][1000 genomes]
rs34147581	1.00[EUR][1000 genomes]
rs35366910	1.00[EUR][1000 genomes]
rs4018904	1.00[EUR][1000 genomes]
rs4282092	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4289375	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4324490	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4373094	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4378998	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4389512	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4450857	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4478107	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4522803	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4543047	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682828	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682832	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682833	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682834	1.00[EUR][1000 genomes]
rs4682835	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682836	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682838	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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683279	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683284	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683285	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683286	0.89[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	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683291	0.91[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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442042	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442043	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442044	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442047	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442048	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442062	1.00[EUR][1000 genomes]
rs6442063	1.00[EUR][1000 genomes]
rs6766676	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	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6804732	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6806521	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	0.89[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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7625011	0.89[AMR][1000 genomes]
rs7630154	1.00[EUR][1000 genomes]
rs7630904	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7638549	0.80[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	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7644382	1.00[EUR][1000 genomes]
rs7646076	1.00[EUR][1000 genomes]
rs7649941	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7650142	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652492	1.00[EUR][1000 genomes]
rs936173	1.00[EUR][1000 genomes]
rs936177	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936178	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936179	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936180	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936181	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	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	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: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	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
5	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
6	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
7	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
8	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
9	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
10	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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46985800-47004400	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr3:46990000-47006800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:46995600-47004200	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr3:46995800-47005200	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr3:46996000-47004200	Enhancers	Primary T cells from cord blood	blood
6	chr3:46996000-47004600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr3:46996000-47004800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:46996000-47007200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:46996400-47005000	Genic enhancers	Primary B cells from peripheral blood	blood
10	chr3:46999200-47004400	Enhancers	Liver	Liver
11	chr3:46999800-47004800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr3:47000000-47004800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr3:47000200-47004800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:47000400-47004800	Genic enhancers	HepG2	liver
15	chr3:47001600-47004200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:47001800-47004800	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr3:47002200-47004800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr3:47002200-47006600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:47002200-47012000	Weak transcription	Osteobl	bone
20	chr3:47002400-47006800	Weak transcription	Small Intestine	intestine
21	chr3:47002400-47007400	Weak transcription	Colonic Mucosa	Colon
22	chr3:47002400-47012000	Weak transcription	NHLF	lung
23	chr3:47002400-47013200	Weak transcription	NH-A	brain
24	chr3:47002600-47004400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:47002800-47004200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:47002800-47006600	Weak transcription	Fetal Brain Female	brain
27	chr3:47003000-47004200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:47003000-47004200	Weak transcription	Fetal Kidney	kidney
29	chr3:47003000-47004800	Enhancers	HUVEC	blood vessel
30	chr3:47003000-47006600	Weak transcription	Placenta	Placenta
31	chr3:47003000-47006800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:47003000-47006800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:47003000-47006800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:47003000-47006800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:47003000-47006800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:47003000-47007000	Weak transcription	HSMMtube	muscle
37	chr3:47003000-47007200	Weak transcription	Hela-S3	cervix
38	chr3:47003000-47010400	Weak transcription	Aorta	Aorta
39	chr3:47003200-47004000	Weak transcription	Primary B cells from cord blood	blood
40	chr3:47003200-47004200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:47003200-47004200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr3:47003200-47004200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:47003200-47004200	Weak transcription	Fetal Muscle Leg	muscle
44	chr3:47003200-47004200	Weak transcription	Fetal Thymus	thymus
45	chr3:47003200-47004200	Weak transcription	Psoas Muscle	Psoas
46	chr3:47003200-47004200	Weak transcription	Right Ventricle	heart
47	chr3:47003200-47004200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:47003200-47004200	Weak transcription	Dnd41	blood
49	chr3:47003200-47004200	Weak transcription	HSMM	muscle
50	chr3:47003200-47004600	Weak transcription	Fetal Intestine Large	intestine

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