Variant report

Variant	rs12653560
Chromosome Location	chr5:146796598-146796599
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11167989	0.84[AMR][1000 genomes]
rs12513884	0.84[AMR][1000 genomes]
rs12514302	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12515377	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12518292	0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12655492	1.00[MEX][hapmap]
rs12657083	1.00[MEX][hapmap]
rs12657176	1.00[MEX][hapmap]
rs12657809	0.80[CHB][hapmap];1.00[EUR][1000 genomes]
rs1432853	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1432854	0.93[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1432855	0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1432856	0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1432857	0.85[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17106590	0.84[AMR][1000 genomes]
rs17106592	0.84[AMR][1000 genomes]
rs17106597	0.84[AMR][1000 genomes]
rs17106606	0.84[AMR][1000 genomes]
rs17106679	0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17106682	0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17106683	0.93[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17106686	0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17106688	0.93[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17106689	0.93[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17106690	0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17106698	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17106701	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17106709	0.91[CHD][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17106713	0.80[CHB][hapmap];0.82[CHD][hapmap];1.00[EUR][1000 genomes]
rs17106716	0.80[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2288800	0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2288805	0.87[CHB][hapmap];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2288809	0.87[CHB][hapmap];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2304043	0.90[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2304047	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2895681	0.84[AMR][1000 genomes]
rs3213857	0.87[CHB][hapmap];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3749721	0.84[AMR][1000 genomes]
rs3792837	0.85[AMR][1000 genomes]
rs3792839	0.93[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs3792840	0.91[CHB][hapmap];0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs3792841	0.87[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3792843	0.93[ASN][1000 genomes]
rs3792844	0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3792845	0.93[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3792846	0.93[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3805533	0.84[AMR][1000 genomes]
rs3805534	0.80[CHB][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3805535	0.80[CHB][hapmap];0.84[ASN][1000 genomes]
rs3805538	0.94[ASN][1000 genomes]
rs3805539	0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3805540	0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3805542	0.88[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3805543	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3805544	0.92[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805545	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816012	0.93[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4642416	0.84[AMR][1000 genomes]
rs6891468	0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6897123	0.80[CHB][hapmap];0.82[CHD][hapmap];1.00[EUR][1000 genomes]
rs972302	0.84[AMR][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	nsv519847	chr5:146166378-146812647	Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv599938	chr5:146169511-146806365	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146767800-146796600	Strong transcription	Brain Germinal Matrix	brain
2	chr5:146769400-146800600	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr5:146769800-146810400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:146770000-146800600	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr5:146770200-146805200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr5:146770200-146810800	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr5:146770400-146796600	Strong transcription	Fetal Brain Female	brain
8	chr5:146770400-146800600	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr5:146770600-146798200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr5:146770600-146800400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
11	chr5:146773600-146800600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:146774000-146799400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
13	chr5:146774200-146796800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr5:146775400-146797000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr5:146777600-146796800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr5:146777600-146800600	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr5:146779800-146798400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr5:146780400-146796800	Weak transcription	Spleen	Spleen
19	chr5:146780800-146796600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr5:146783400-146800800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:146784400-146797000	Weak transcription	Brain Angular Gyrus	brain
22	chr5:146784600-146796800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr5:146784600-146796800	Weak transcription	Colonic Mucosa	Colon
24	chr5:146784600-146797000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:146784600-146797000	Weak transcription	Esophagus	oesophagus
26	chr5:146784600-146800400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:146784800-146807400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:146785400-146808800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr5:146787000-146798800	Weak transcription	Right Ventricle	heart
30	chr5:146787400-146796600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr5:146789000-146798000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr5:146791000-146796600	Weak transcription	Fetal Intestine Small	intestine
33	chr5:146791000-146796800	Weak transcription	Left Ventricle	heart
34	chr5:146791200-146796800	Strong transcription	Fetal Muscle Trunk	muscle
35	chr5:146791200-146798200	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr5:146791400-146796600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr5:146791400-146796800	Weak transcription	Right Atrium	heart
38	chr5:146791600-146797800	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr5:146792600-146798800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:146793000-146797000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr5:146793400-146796600	Weak transcription	NHDF-Ad	bronchial
42	chr5:146794400-146796600	Weak transcription	Psoas Muscle	Psoas
43	chr5:146795000-146797800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:146795200-146796600	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr5:146795400-146796600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr5:146795400-146796600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr5:146795400-146796600	Weak transcription	Adipose Nuclei	Adipose
48	chr5:146795400-146796600	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr5:146795400-146796800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr5:146795400-146796800	Weak transcription	Brain Anterior Caudate	brain

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