Variant report

Variant	rs4289375
Chromosome Location	chr3:46986329-46986330
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46949218..46952084-chr3:46985119..46987583,2	K562	blood:
2	chr3:46985961..46989571-chr3:47058662..47060411,3	K562	blood:
3	chr3:46983747..46991522-chr3:47014474..47023916,13	MCF-7	breast:
4	chr3:46984582..46987726-chr3:46988178..46990594,3	K562	blood:
5	chr3:46968433..46974874-chr3:46985986..46991697,10	MCF-7	breast:
6	chr3:46983607..46987334-chr3:46993451..46998407,5	K562	blood:

Variant related genes	Relation type
ENSG00000160796	Chromatin interaction
ENSG00000160799	Chromatin interaction

Extended variants
information (count: 157 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10461017	0.87[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10461019	0.86[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10865945	1.00[EUR][1000 genomes]
rs11130108	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11130109	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11706212	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11708257	0.86[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11709693	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11709876	0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11713537	0.86[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11922925	1.00[EUR][1000 genomes]
rs11928558	0.82[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12330516	1.00[EUR][1000 genomes]
rs12487763	0.81[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12488371	1.00[EUR][1000 genomes]
rs12631730	0.81[YRI][hapmap]
rs13062185	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13078181	1.00[EUR][1000 genomes]
rs13079416	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13082531	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13323092	1.00[EUR][1000 genomes]
rs1378818	0.87[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1463394	0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466272	0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466273	0.83[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466274	0.83[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1473382	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1473384	1.00[EUR][1000 genomes]
rs1473385	1.00[EUR][1000 genomes]
rs1563431	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1563432	1.00[EUR][1000 genomes]
rs1814564	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1869870	0.81[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1979736	1.00[EUR][1000 genomes]
rs2124509	0.87[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2124510	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2350642	1.00[EUR][1000 genomes]
rs2385863	1.00[EUR][1000 genomes]
rs2385868	0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2385869	0.87[YRI][hapmap];0.89[AMR][1000 genomes]
rs2385872	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs28735306	1.00[EUR][1000 genomes]
rs2891887	0.89[AMR][1000 genomes]
rs2891893	0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs34147581	1.00[EUR][1000 genomes]
rs35366910	1.00[EUR][1000 genomes]
rs4018904	0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs4282092	0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs4324490	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4373094	0.87[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4378998	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4389512	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4450857	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4478107	0.81[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4522803	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4525902	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4543047	0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682828	1.00[EUR][1000 genomes]
rs4682832	0.95[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682833	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682834	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4682835	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682836	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682838	0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682841	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682843	0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682846	1.00[EUR][1000 genomes]
rs4682847	1.00[EUR][1000 genomes]
rs4683277	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683279	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683282	0.95[YRI][hapmap]
rs4683283	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683284	0.86[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683285	0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683286	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683288	1.00[EUR][1000 genomes]
rs4683289	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683290	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683291	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683292	0.86[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683293	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683303	1.00[EUR][1000 genomes]
rs6442041	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442042	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442043	0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442044	0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442047	0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442048	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442062	1.00[EUR][1000 genomes]
rs6442063	1.00[EUR][1000 genomes]
rs6766676	0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6767868	1.00[EUR][1000 genomes]
rs6768169	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6775797	1.00[EUR][1000 genomes]
rs6780994	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6785462	0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6804732	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6806521	0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808052	1.00[EUR][1000 genomes]
rs6808629	1.00[EUR][1000 genomes]
rs6809904	0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831482	1.00[EUR][1000 genomes]
rs7615774	1.00[EUR][1000 genomes]
rs7621530	0.83[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7624549	0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7625011	0.95[YRI][hapmap]
rs7630154	0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs7630904	0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7638549	0.86[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7641494	1.00[EUR][1000 genomes]
rs7643868	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7644382	1.00[EUR][1000 genomes]
rs7646076	0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7649941	0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7650142	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[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];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936178	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936179	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936180	0.95[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936181	0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936182	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936185	1.00[EUR][1000 genomes]
rs936186	0.83[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9637426	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9810881	0.89[AMR][1000 genomes];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:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46971200-46988400	Strong transcription	Dnd41	blood
2	chr3:46974000-46988600	Strong transcription	Primary T cells from cord blood	blood
3	chr3:46976200-46990200	Weak transcription	Fetal Brain Male	brain
4	chr3:46977000-47000000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:46978000-46990600	Strong transcription	Fetal Stomach	stomach
6	chr3:46979400-46989200	Weak transcription	NHDF-Ad	bronchial
7	chr3:46979600-46994600	Genic enhancers	Fetal Thymus	thymus
8	chr3:46980200-46990800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:46981600-46986800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:46982200-46987800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:46982200-46989000	Weak transcription	HSMMtube	muscle
12	chr3:46982400-46986600	Weak transcription	Osteobl	bone
13	chr3:46982400-46987400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:46982400-46987800	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr3:46982400-46988600	Enhancers	Stomach Mucosa	stomach
16	chr3:46982400-46989000	Weak transcription	Aorta	Aorta
17	chr3:46982600-46988600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:46982600-46988800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:46982600-46988800	Weak transcription	NHLF	lung
20	chr3:46982600-46989000	Weak transcription	Brain Germinal Matrix	brain
21	chr3:46982800-46986800	Enhancers	Fetal Intestine Large	intestine
22	chr3:46982800-46992600	Enhancers	Left Ventricle	heart
23	chr3:46983000-46987000	Genic enhancers	Fetal Muscle Trunk	muscle
24	chr3:46983000-46989400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:46983000-46992600	Enhancers	Small Intestine	intestine
26	chr3:46983200-46986600	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr3:46983200-46989400	Enhancers	HMEC	breast
28	chr3:46983200-46989600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr3:46983200-46992400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr3:46983400-46991200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:46983600-46986800	Genic enhancers	Primary T cells fromperipheralblood	blood
32	chr3:46983600-46987400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:46983600-46987400	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr3:46983600-46992600	Enhancers	Psoas Muscle	Psoas
35	chr3:46983600-46992600	Enhancers	Right Atrium	heart
36	chr3:46983600-46994000	Enhancers	HUVEC	blood vessel
37	chr3:46983800-46987200	Enhancers	Fetal Lung	lung
38	chr3:46983800-46987400	Enhancers	Lung	lung
39	chr3:46984000-46987000	Genic enhancers	Fetal Muscle Leg	muscle
40	chr3:46984000-46989200	Weak transcription	Fetal Brain Female	brain
41	chr3:46984000-46989400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:46984200-46986600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:46984200-46986600	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr3:46984200-46986800	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr3:46984200-46986800	Enhancers	Stomach Smooth Muscle	stomach
46	chr3:46984200-46987000	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr3:46984200-46987000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:46984200-46987000	Enhancers	Adipose Nuclei	Adipose
49	chr3:46984200-46987000	Enhancers	Placenta	Placenta
50	chr3:46984200-46987200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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