Variant report

Variant	rs55662129
Chromosome Location	chr3:98578214-98578215
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10433438	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511169	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511171	0.86[ASN][1000 genomes]
rs10935518	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935542	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935564	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11708475	0.91[ASN][1000 genomes]
rs11716000	0.91[ASN][1000 genomes]
rs11716007	0.91[ASN][1000 genomes]
rs11716281	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11716579	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719660	0.91[ASN][1000 genomes]
rs11914591	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11914715	0.93[EUR][1000 genomes]
rs11916285	0.97[EUR][1000 genomes]
rs11918243	0.97[ASN][1000 genomes]
rs11918944	0.91[ASN][1000 genomes]
rs11920205	0.91[ASN][1000 genomes]
rs11920327	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11922078	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11923486	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11923805	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11928233	0.91[ASN][1000 genomes]
rs12203	0.94[EUR][1000 genomes]
rs13069458	0.91[ASN][1000 genomes]
rs1440154	0.97[EUR][1000 genomes]
rs1471588	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16840260	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846347	0.92[EUR][1000 genomes]
rs17210963	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17212369	0.97[ASN][1000 genomes]
rs17213336	0.91[ASN][1000 genomes]
rs17278047	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17278278	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17852693	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1822017	0.94[EUR][1000 genomes]
rs1827158	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278599	0.94[EUR][1000 genomes]
rs3772100	0.93[EUR][1000 genomes]
rs55650073	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55730510	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55764252	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55988144	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56075614	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56290036	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56322058	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276861	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276862	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62276864	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276869	0.91[ASN][1000 genomes]
rs62276879	0.85[ASN][1000 genomes]
rs62276883	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276884	0.91[ASN][1000 genomes]
rs62276885	0.91[ASN][1000 genomes]
rs62276888	0.91[ASN][1000 genomes]
rs62276909	0.88[ASN][1000 genomes]
rs6440159	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6440253	0.91[ASN][1000 genomes]
rs66517942	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6805605	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136038	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73136045	0.94[EUR][1000 genomes]
rs73136048	0.94[EUR][1000 genomes]
rs73136057	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73136060	0.93[EUR][1000 genomes]
rs73138004	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73138027	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138048	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138053	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138055	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138058	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73138063	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138082	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73140009	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73140027	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73140032	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7432439	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7614892	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629550	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638009	0.91[ASN][1000 genomes]
rs7642785	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644946	0.97[EUR][1000 genomes]
rs8179927	0.97[EUR][1000 genomes]
rs982291	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98536200-98594200	Weak transcription	HepG2	liver
2	chr3:98537000-98592800	Weak transcription	K562	blood
3	chr3:98552800-98579800	Weak transcription	Right Ventricle	heart
4	chr3:98553000-98590600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:98567600-98601000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr3:98572400-98579200	Weak transcription	Brain Angular Gyrus	brain
7	chr3:98573000-98579200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:98574600-98582400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:98575000-98579400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:98575200-98578400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:98575200-98590200	Weak transcription	HSMMtube	muscle
12	chr3:98575400-98578400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
13	chr3:98575400-98579200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:98575400-98583800	Weak transcription	HSMM	muscle
15	chr3:98575400-98603800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:98575600-98579000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:98575600-98583600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:98575800-98578800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:98575800-98583600	Weak transcription	NH-A	brain
20	chr3:98575800-98583600	Weak transcription	Osteobl	bone
21	chr3:98575800-98593200	Weak transcription	HUVEC	blood vessel
22	chr3:98575800-98603200	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:98575800-98603800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr3:98576000-98589800	Weak transcription	HMEC	breast
25	chr3:98576000-98590400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:98576000-98598600	Weak transcription	Fetal Kidney	kidney
27	chr3:98576200-98579000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:98576600-98583000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:98576800-98578400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:98576800-98578800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:98576800-98578800	Weak transcription	Primary T cells from cord blood	blood
32	chr3:98577200-98583200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:98577200-98598800	Weak transcription	Left Ventricle	heart
34	chr3:98577400-98578800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:98577400-98579000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:98578000-98578800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:98578000-98578800	Strong transcription	A549	lung
38	chr3:98578000-98583600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:98578000-98583600	Weak transcription	Dnd41	blood
40	chr3:98578000-98587400	Weak transcription	NHEK	skin
41	chr3:98578000-98588800	Weak transcription	NHLF	lung
42	chr3:98578000-98590400	Weak transcription	Adipose Nuclei	Adipose
43	chr3:98578000-98601000	Weak transcription	Lung	lung
44	chr3:98578200-98578600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:98578200-98579200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:98578200-98586400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:98578200-98590400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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