Variant report

Variant	rs62261539
Chromosome Location	chr3:105515184-105515185
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12054270	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12487349	0.84[ASN][1000 genomes]
rs12493071	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12493771	0.81[ASN][1000 genomes]
rs1443100	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16851512	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16851553	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16851673	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16851707	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1814078	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1867194	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2028598	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2028599	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2055558	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2055559	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2120103	0.92[AMR][1000 genomes]
rs2120104	0.90[ASN][1000 genomes]
rs2301028	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2301034	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2301035	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3213928	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34360428	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35909361	0.93[ASN][1000 genomes]
rs3772517	0.93[ASN][1000 genomes]
rs3772522	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3772525	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3821490	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4431143	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4469007	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4894956	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62255570	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62255571	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62255572	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62255573	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62255575	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62256353	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62258160	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261460	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261462	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261487	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261489	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261491	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261492	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261493	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261495	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261496	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261497	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261498	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261499	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261538	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263056	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62263057	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62263059	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62263169	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263170	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62264260	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6809776	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7619706	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628896	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7631219	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641527	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7650046	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs964173	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9657903	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9657924	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs971109	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849559	0.90[ASN][1000 genomes]
rs9856147	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105482800-105517400	Weak transcription	Fetal Intestine Large	intestine
2	chr3:105483200-105555200	Weak transcription	Placenta	Placenta
3	chr3:105486800-105519000	Weak transcription	Esophagus	oesophagus
4	chr3:105489600-105525400	Weak transcription	Fetal Intestine Small	intestine
5	chr3:105494400-105516200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:105495400-105517200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:105501800-105516600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:105505000-105527800	Weak transcription	Pancreas	Pancrea
9	chr3:105505000-105548200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:105505600-105517400	Weak transcription	Brain Substantia Nigra	brain
11	chr3:105506200-105516000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:105506600-105518200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:105509800-105527800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr3:105510000-105517400	Weak transcription	Stomach Mucosa	stomach
15	chr3:105510200-105516400	Weak transcription	Primary T cells from cord blood	blood
16	chr3:105510600-105521200	Weak transcription	Fetal Brain Male	brain
17	chr3:105511400-105566400	Weak transcription	Aorta	Aorta
18	chr3:105511600-105515200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr3:105511600-105516600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:105511600-105516800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr3:105511800-105520400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:105512000-105516800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:105512000-105516800	Weak transcription	NH-A	brain
24	chr3:105512000-105520600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:105512200-105516200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:105512200-105516200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:105512200-105516600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:105512200-105517200	Weak transcription	Fetal Lung	lung
29	chr3:105512200-105517400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:105512200-105517400	Weak transcription	Fetal Heart	heart
31	chr3:105512200-105517400	Weak transcription	Ovary	ovary
32	chr3:105512200-105517400	Weak transcription	Small Intestine	intestine
33	chr3:105512200-105519000	Weak transcription	Psoas Muscle	Psoas
34	chr3:105512200-105519000	Weak transcription	Right Atrium	heart
35	chr3:105512200-105519200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr3:105512200-105520200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:105512200-105520400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr3:105512200-105527200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr3:105512200-105534200	Weak transcription	Left Ventricle	heart
40	chr3:105512400-105524400	Weak transcription	NHLF	lung
41	chr3:105512600-105516800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:105512600-105518200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:105512600-105520400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr3:105512600-105524000	Weak transcription	HSMMtube	muscle
45	chr3:105512600-105524600	Weak transcription	Colon Smooth Muscle	Colon
46	chr3:105512600-105525200	Weak transcription	HSMM	muscle
47	chr3:105512800-105517400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:105512800-105517400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:105512800-105517400	Weak transcription	A549	lung
50	chr3:105513000-105515600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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