Variant report

Variant	rs964173
Chromosome Location	chr3:105489534-105489535
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs12054270	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12487349	0.87[ASN][1000 genomes]
rs12493071	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12493771	0.81[ASN][1000 genomes]
rs1443100	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16851512	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16851553	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16851673	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16851707	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1814078	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1867194	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2028598	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028599	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055558	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2055559	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2120103	0.88[AMR][1000 genomes]
rs2120104	0.88[ASN][1000 genomes]
rs2301028	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2301034	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2301035	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3213928	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34360428	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35909361	0.90[ASN][1000 genomes]
rs3772517	0.96[ASN][1000 genomes]
rs3772522	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3772525	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821490	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4431143	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4469007	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4894956	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62255570	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62255571	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62255572	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62255573	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62255575	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62256353	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62258160	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261460	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261462	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261487	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261489	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261491	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261492	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261493	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261495	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261496	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261497	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261498	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261499	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261538	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261539	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62263056	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62263057	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62263059	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62263169	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62263170	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62264260	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6809776	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7619706	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7628896	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7631219	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7641527	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7650046	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9657903	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9657924	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs971109	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9849559	0.88[ASN][1000 genomes]
rs9856147	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][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	chr3:105478800-105496200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:105481200-105500800	Weak transcription	Small Intestine	intestine
9	chr3:105481400-105491600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:105481400-105509600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:105481600-105498000	Weak transcription	NH-A	brain
12	chr3:105481800-105507400	Weak transcription	HSMM	muscle
13	chr3:105482000-105492400	Weak transcription	HepG2	liver
14	chr3:105482000-105496200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:105482000-105496200	Weak transcription	Lung	lung
16	chr3:105482000-105503800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:105482000-105509200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:105482000-105509600	Weak transcription	Ovary	ovary
19	chr3:105482000-105510800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:105482000-105511200	Weak transcription	Aorta	Aorta
21	chr3:105482200-105494600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr3:105482400-105489800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:105482400-105493600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:105482400-105494400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:105482400-105500000	Weak transcription	Fetal Stomach	stomach
26	chr3:105482800-105517400	Weak transcription	Fetal Intestine Large	intestine
27	chr3:105483000-105491400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:105483200-105506200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:105483200-105555200	Weak transcription	Placenta	Placenta
30	chr3:105484200-105491600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:105484800-105491600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:105484800-105494600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:105485200-105492400	Weak transcription	Osteobl	bone
34	chr3:105485600-105491400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:105486800-105492600	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr3:105486800-105493000	Weak transcription	Primary hematopoietic stem cells	blood
37	chr3:105486800-105493200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:105486800-105519000	Weak transcription	Esophagus	oesophagus
39	chr3:105487000-105491000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr3:105487000-105491200	Weak transcription	Primary B cells from peripheral blood	blood
41	chr3:105487000-105492800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:105487000-105493200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr3:105487000-105497400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:105487000-105508400	Weak transcription	Fetal Lung	lung
45	chr3:105487200-105493000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:105487200-105508400	Weak transcription	Fetal Kidney	kidney
47	chr3:105487400-105494400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:105487400-105494800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr3:105487400-105500600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:105487400-105504200	Weak transcription	Fetal Heart	heart

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