Variant report

Variant	rs62137573
Chromosome Location	chr2:53955471-53955472
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10490468	0.92[ASN][1000 genomes]
rs11897282	0.99[ASN][1000 genomes]
rs11901698	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs13408029	0.93[ASN][1000 genomes]
rs17045176	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17045203	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17520505	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs17520854	0.85[AMR][1000 genomes]
rs17521008	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2008082	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2287340	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2302797	0.99[ASN][1000 genomes]
rs2542572	0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2542573	0.84[ASN][1000 genomes]
rs2542578	0.91[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2542580	0.84[ASN][1000 genomes]
rs2542581	0.80[AFR][1000 genomes]
rs2542583	0.81[ASN][1000 genomes]
rs2542589	0.86[ASN][1000 genomes]
rs2542590	0.86[ASN][1000 genomes]
rs2542591	0.86[ASN][1000 genomes]
rs2542592	0.83[ASN][1000 genomes]
rs2543629	0.85[ASN][1000 genomes]
rs2692512	0.82[ASN][1000 genomes]
rs2692513	0.82[ASN][1000 genomes]
rs2692519	0.87[ASN][1000 genomes]
rs2692521	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2692522	0.84[ASN][1000 genomes]
rs2692523	0.91[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2692533	0.80[ASN][1000 genomes]
rs2692535	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2909262	0.83[ASN][1000 genomes]
rs2949813	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35772199	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3770394	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3770395	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3770397	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770399	0.99[ASN][1000 genomes]
rs3770411	0.88[ASN][1000 genomes]
rs3922262	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4116709	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs55897904	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56214822	0.87[ASN][1000 genomes]
rs58326257	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62137565	0.83[ASN][1000 genomes]
rs62137602	0.96[ASN][1000 genomes]
rs62137605	0.86[ASN][1000 genomes]
rs62137606	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62137610	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62137611	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62137612	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6730006	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs719127	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs72901256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7558968	0.87[ASN][1000 genomes]
rs7600817	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs805435	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916267	chr2:53747525-53955999	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers 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	20 gene(s)	inside rSNPs	diseases
4	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	esv1844655	chr2:53929855-53972693	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53898000-53957400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:53908600-53982200	Weak transcription	Small Intestine	intestine
3	chr2:53910000-53994000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:53910200-53990600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:53918400-53994000	Weak transcription	Fetal Heart	heart
6	chr2:53925400-53979400	Weak transcription	Psoas Muscle	Psoas
7	chr2:53927600-53960200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:53936600-53968400	Weak transcription	Pancreas	Pancrea
9	chr2:53936600-53978600	Weak transcription	Hela-S3	cervix
10	chr2:53936800-53985400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr2:53937000-53983800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:53937000-53994400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:53937200-53955800	Weak transcription	Brain Substantia Nigra	brain
14	chr2:53937200-53961400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:53937200-53964400	Weak transcription	Aorta	Aorta
16	chr2:53937200-53966800	Weak transcription	Gastric	stomach
17	chr2:53937200-53978600	Weak transcription	NH-A	brain
18	chr2:53937200-53983600	Weak transcription	Right Ventricle	heart
19	chr2:53937200-53994200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:53937400-53964000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:53937400-53979600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:53937400-53990200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr2:53937400-53994400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr2:53937600-53961600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:53937800-53957000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:53938000-53956400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr2:53938000-53961400	Weak transcription	NHEK	skin
28	chr2:53938000-53974800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr2:53938000-53974800	Weak transcription	Placenta	Placenta
30	chr2:53938200-53967000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:53938200-53975200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr2:53938400-53963600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:53938400-53969400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr2:53938400-53969600	Weak transcription	Esophagus	oesophagus
35	chr2:53938400-53975000	Weak transcription	Fetal Kidney	kidney
36	chr2:53938400-53982800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr2:53938400-53983400	Weak transcription	HSMMtube	muscle
38	chr2:53938400-53992400	Weak transcription	K562	blood
39	chr2:53938600-53961000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:53938600-53972000	Weak transcription	HSMM	muscle
41	chr2:53940600-53957400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:53941600-53956400	Weak transcription	GM12878-XiMat	blood
43	chr2:53941800-53956400	Weak transcription	Brain Angular Gyrus	brain
44	chr2:53941800-53957400	Weak transcription	Liver	Liver
45	chr2:53941800-53974400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:53941800-53976400	Weak transcription	Colon Smooth Muscle	Colon
47	chr2:53943800-53960600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:53943800-53974800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr2:53943800-53983600	Weak transcription	Ovary	ovary
50	chr2:53943800-53983600	Weak transcription	Thymus	Thymus

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