Variant report

Variant	rs2389884
Chromosome Location	chr4:120530449-120530450
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10013852	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021469	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10434030	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10434031	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10434032	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10518332	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10518333	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11932826	0.81[AFR][1000 genomes]
rs12331661	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12331968	0.83[AFR][1000 genomes]
rs13119104	1.00[AFR][1000 genomes]
rs13122502	0.85[AFR][1000 genomes]
rs13125819	1.00[AFR][1000 genomes]
rs17007472	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17051276	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17051278	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17357002	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17359764	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17359910	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17360333	0.90[EUR][1000 genomes]
rs2256645	0.93[AFR][1000 genomes]
rs2389865	0.85[AFR][1000 genomes]
rs2389867	0.85[AFR][1000 genomes]
rs2389872	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389876	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389877	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389878	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2622497	0.93[AFR][1000 genomes]
rs2715020	0.85[AFR][1000 genomes]
rs2715021	0.80[AFR][1000 genomes]
rs2715022	0.85[AFR][1000 genomes]
rs2928991	1.00[AFR][1000 genomes]
rs2953290	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2953292	0.85[AFR][1000 genomes]
rs2953294	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3109370	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4102980	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4146266	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4264816	0.85[AFR][1000 genomes]
rs4513554	0.85[AFR][1000 genomes]
rs4833621	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4834786	0.96[AFR][1000 genomes]
rs4834787	0.96[AFR][1000 genomes]
rs58613543	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58735454	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534136	0.83[AFR][1000 genomes]
rs6534145	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534148	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827780	0.89[AFR][1000 genomes]
rs6831062	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845402	0.89[AFR][1000 genomes]
rs6848530	0.81[AFR][1000 genomes]
rs6854072	0.82[AFR][1000 genomes]
rs72922580	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72922588	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72922598	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7439678	1.00[AFR][1000 genomes]
rs7665086	0.81[AFR][1000 genomes]
rs7694813	0.96[AFR][1000 genomes]
rs7697823	0.85[AFR][1000 genomes]
rs8180145	0.90[ASN][1000 genomes]
rs8180147	0.90[ASN][1000 genomes]
rs9307480	0.94[AFR][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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120492200-120540000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr4:120502600-120541000	Weak transcription	Left Ventricle	heart
3	chr4:120512800-120531600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:120517000-120531400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr4:120517000-120536600	Weak transcription	Ovary	ovary
6	chr4:120518800-120547200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr4:120519000-120533400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:120520200-120536400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:120520400-120533200	Weak transcription	Fetal Intestine Small	intestine
10	chr4:120520400-120537600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr4:120521000-120544800	Weak transcription	Fetal Intestine Large	intestine
12	chr4:120525400-120531200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr4:120525800-120538800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:120526200-120546800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:120526400-120530600	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:120526400-120544200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr4:120526600-120532600	Weak transcription	Fetal Lung	lung
18	chr4:120526600-120535400	Weak transcription	Fetal Brain Male	brain
19	chr4:120527400-120536400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:120528200-120531400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr4:120528400-120532200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:120528400-120532200	Weak transcription	Lung	lung
23	chr4:120528400-120532600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr4:120528400-120547400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr4:120528600-120531400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:120528600-120531600	Weak transcription	Osteobl	bone
27	chr4:120528600-120532600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr4:120528600-120533200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:120528600-120533400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:120528600-120547400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr4:120528600-120547600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:120528800-120531200	Weak transcription	Aorta	Aorta
33	chr4:120528800-120531800	Weak transcription	NHLF	lung
34	chr4:120528800-120533800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr4:120528800-120539000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr4:120528800-120540200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr4:120528800-120543000	Weak transcription	Pancreas	Pancrea
38	chr4:120528800-120544200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr4:120528800-120545400	Weak transcription	Fetal Stomach	stomach
40	chr4:120529000-120546600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr4:120530200-120531600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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