Variant report

Variant	rs3754539
Chromosome Location	chr2:63626173-63626174
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10182889	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10191163	0.87[ASN][1000 genomes]
rs10195862	0.88[ASN][1000 genomes]
rs1022352	0.93[ASN][1000 genomes]
rs11125968	0.94[ASN][1000 genomes]
rs11687234	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11694795	0.96[ASN][1000 genomes]
rs11694892	0.96[ASN][1000 genomes]
rs12465146	0.93[ASN][1000 genomes]
rs12470121	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12473110	0.91[ASN][1000 genomes]
rs12473300	0.93[ASN][1000 genomes]
rs12478262	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12987806	0.92[ASN][1000 genomes]
rs12996604	0.89[ASN][1000 genomes]
rs13020863	0.93[ASN][1000 genomes]
rs1568174	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1807843	0.96[ASN][1000 genomes]
rs1810333	0.93[ASN][1000 genomes]
rs1966112	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2028886	0.89[ASN][1000 genomes]
rs2034270	0.90[ASN][1000 genomes]
rs2138793	0.94[ASN][1000 genomes]
rs2138794	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2176414	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2421888	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2901581	0.88[ASN][1000 genomes]
rs35516797	0.90[ASN][1000 genomes]
rs4471880	0.92[ASN][1000 genomes]
rs4671501	0.93[ASN][1000 genomes]
rs4671502	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4671504	0.93[ASN][1000 genomes]
rs4671506	0.92[ASN][1000 genomes]
rs4671507	0.93[ASN][1000 genomes]
rs62177834	0.96[ASN][1000 genomes]
rs6546003	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6745644	0.93[ASN][1000 genomes]
rs6756605	0.93[ASN][1000 genomes]
rs6756696	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6761544	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs72883636	0.86[ASN][1000 genomes]
rs9749852	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9749863	0.88[ASN][1000 genomes]
rs9749870	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9751845	0.83[AFR][1000 genomes];0.87[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	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1006848	chr2:63061816-63631407	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv535768	chr2:63413596-63631407	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv1800788	chr2:63473443-63900292	ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv834241	chr2:63490262-63668205	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1002047	chr2:63584797-63648782	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv874234	chr2:63606001-63666590	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv874235	chr2:63622470-63709708	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63595200-63631200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr2:63597800-63649200	Weak transcription	Fetal Lung	lung
3	chr2:63598800-63631200	Weak transcription	Dnd41	blood
4	chr2:63599000-63631000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:63599400-63631200	Weak transcription	Aorta	Aorta
6	chr2:63599400-63631600	Weak transcription	Pancreas	Pancrea
7	chr2:63599800-63631200	Weak transcription	Thymus	Thymus
8	chr2:63605000-63642400	Weak transcription	HSMMtube	muscle
9	chr2:63605600-63631200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:63605800-63631200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:63606000-63632800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:63607600-63631200	Weak transcription	Right Ventricle	heart
13	chr2:63615600-63631200	Weak transcription	Lung	lung
14	chr2:63615600-63637000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr2:63615800-63637000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:63620000-63631000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr2:63621000-63630000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:63621000-63630000	Weak transcription	Brain Anterior Caudate	brain
19	chr2:63621400-63637000	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:63621600-63633000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr2:63622000-63630800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:63622200-63645400	Weak transcription	Liver	Liver
23	chr2:63622800-63626400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:63622800-63630800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr2:63622800-63635600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:63623000-63633000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:63623400-63632800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:63623800-63626400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr2:63624400-63631200	Weak transcription	Ovary	ovary
30	chr2:63624600-63629200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:63624800-63642400	Weak transcription	Left Ventricle	heart
32	chr2:63625000-63626800	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr2:63625200-63631000	Weak transcription	Primary B cells from cord blood	blood
34	chr2:63625200-63631200	Weak transcription	Primary T cells from cord blood	blood
35	chr2:63625400-63630000	Weak transcription	Adipose Nuclei	Adipose
36	chr2:63625600-63627600	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr2:63625800-63627200	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr2:63626000-63627200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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