Variant report

Variant	rs4613490
Chromosome Location	chr3:105488254-105488255
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1020327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1025885	1.00[AMR][1000 genomes]
rs1025886	1.00[AMR][1000 genomes]
rs1036877	1.00[AMR][1000 genomes]
rs1039545	1.00[AMR][1000 genomes]
rs10933832	1.00[AMR][1000 genomes]
rs1348348	1.00[AMR][1000 genomes]
rs1443099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1443107	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1503922	1.00[AMR][1000 genomes]
rs1548056	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1561920	1.00[AMR][1000 genomes]
rs1822348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1838045	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1867428	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1867429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1963622	1.00[AMR][1000 genomes]
rs1992520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2197351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2221379	1.00[AMR][1000 genomes]
rs3862049	1.00[AMR][1000 genomes]
rs4243428	1.00[AMR][1000 genomes]
rs4282093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4894945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4894947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4894948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4894959	1.00[AMR][1000 genomes]
rs4894961	1.00[AMR][1000 genomes]
rs6437615	1.00[AMR][1000 genomes]
rs6437617	1.00[AMR][1000 genomes]
rs6437625	1.00[AMR][1000 genomes]
rs6765716	1.00[AMR][1000 genomes]
rs6768096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6804286	1.00[AMR][1000 genomes]
rs6805675	1.00[AMR][1000 genomes]
rs7622735	1.00[AMR][1000 genomes]
rs7643647	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7649437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9288816	1.00[AMR][1000 genomes]
rs9288819	1.00[AMR][1000 genomes]
rs9288820	1.00[AMR][1000 genomes]
rs976961	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs976962	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9809911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9811870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs981479	1.00[AMR][1000 genomes]
rs9830539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9831221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9833645	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9838768	1.00[AMR][1000 genomes]
rs9859644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9872290	1.00[AFR][1000 genomes];1.00[AMR][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	nsv877306	chr3:105372196-105495841	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv877308	chr3:105373836-105495841	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv877309	chr3:105373836-105542435	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv877310	chr3:105409321-105495841	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv591244	chr3:105438320-105495841	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv591246	chr3:105439522-105504129	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv877311	chr3:105449986-105493286	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105467600-105509400	Weak transcription	Stomach Mucosa	stomach
2	chr3:105472200-105499000	Weak transcription	NHDF-Ad	bronchial
3	chr3:105472400-105504400	Weak transcription	HUVEC	blood vessel
4	chr3:105478200-105495400	Weak transcription	HSMMtube	muscle
5	chr3:105478600-105509400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:105478600-105511200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:105478800-105489200	Weak transcription	Right Atrium	heart
8	chr3:105478800-105496200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:105481200-105500800	Weak transcription	Small Intestine	intestine
10	chr3:105481400-105491600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:105481400-105509600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:105481600-105498000	Weak transcription	NH-A	brain
13	chr3:105481800-105507400	Weak transcription	HSMM	muscle
14	chr3:105482000-105492400	Weak transcription	HepG2	liver
15	chr3:105482000-105496200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:105482000-105496200	Weak transcription	Lung	lung
17	chr3:105482000-105503800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:105482000-105509200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:105482000-105509600	Weak transcription	Ovary	ovary
20	chr3:105482000-105510800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:105482000-105511200	Weak transcription	Aorta	Aorta
22	chr3:105482200-105494600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr3:105482400-105489400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr3:105482400-105489800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:105482400-105493600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:105482400-105494400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:105482400-105500000	Weak transcription	Fetal Stomach	stomach
28	chr3:105482800-105489000	Weak transcription	Fetal Intestine Small	intestine
29	chr3:105482800-105489400	Weak transcription	Fetal Muscle Leg	muscle
30	chr3:105482800-105517400	Weak transcription	Fetal Intestine Large	intestine
31	chr3:105483000-105491400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:105483200-105506200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:105483200-105555200	Weak transcription	Placenta	Placenta
34	chr3:105483800-105489400	Weak transcription	Right Ventricle	heart
35	chr3:105484000-105489000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:105484200-105491600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:105484800-105491600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:105484800-105494600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:105485200-105492400	Weak transcription	Osteobl	bone
40	chr3:105485600-105491400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:105486400-105488800	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr3:105486800-105488400	Weak transcription	GM12878-XiMat	blood
43	chr3:105486800-105492600	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr3:105486800-105493000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr3:105486800-105493200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr3:105486800-105519000	Weak transcription	Esophagus	oesophagus
47	chr3:105487000-105489000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:105487000-105489000	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr3:105487000-105489000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:105487000-105489000	Weak transcription	Left Ventricle	heart

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