Variant report

Variant	rs604662
Chromosome Location	chr12:48023014-48023015
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10875666	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875677	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10875682	0.82[EUR][1000 genomes]
rs11168167	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168191	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11168192	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11168193	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11168199	0.83[EUR][1000 genomes]
rs11168200	0.82[EUR][1000 genomes]
rs11168203	0.81[EUR][1000 genomes]
rs12366410	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12367193	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12370643	0.85[ASN][1000 genomes]
rs1541384	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56011001	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56240307	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs582680	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs583752	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs602143	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs605499	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs611627	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs612773	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61917590	0.85[ASN][1000 genomes]
rs61917591	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61917594	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61917595	0.83[EUR][1000 genomes]
rs622098	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs623894	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs630777	0.87[ASN][1000 genomes]
rs632944	0.87[ASN][1000 genomes]
rs634833	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs642453	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs644531	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs646223	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs652380	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs653136	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs658567	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs659836	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs668968	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs671961	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs679789	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs687676	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7136143	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7136561	0.83[EUR][1000 genomes]
rs7137529	0.85[ASN][1000 genomes]
rs7316761	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs739858	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7954502	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7968783	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7977786	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs864112	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558785	chr12:47740440-48044011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	nsv832400	chr12:47840248-48024605	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv430507	chr12:47883933-48079507	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2751101	chr12:47940858-48126885	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv558786	chr12:47942029-48044011	Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv2761737	chr12:47946795-48045722	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1053061	chr12:47946795-48045722	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1050043	chr12:47949004-48087218	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv527728	chr12:47954597-48044506	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv899058	chr12:48012390-48082482	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs604662	ENDOU	cis	Thyroid	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47998800-48030800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:48007200-48024600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:48007400-48041800	Weak transcription	HSMMtube	muscle
4	chr12:48007400-48044800	Weak transcription	Aorta	Aorta
5	chr12:48007400-48055400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:48007600-48028200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:48007600-48032000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:48007600-48037600	Weak transcription	Left Ventricle	heart
9	chr12:48008400-48029000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:48008600-48033400	Weak transcription	Pancreas	Pancrea
11	chr12:48009000-48023600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr12:48009000-48032200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:48009800-48036200	Weak transcription	Ovary	ovary
14	chr12:48010200-48027800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr12:48011600-48029600	Weak transcription	HSMM	muscle
16	chr12:48012800-48024400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:48013000-48024400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:48013000-48025600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:48013000-48029000	Weak transcription	Primary B cells from cord blood	blood
20	chr12:48013200-48024200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:48013400-48024200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:48013400-48024600	Weak transcription	A549	lung
23	chr12:48014200-48025400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:48014600-48029200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:48014800-48030600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:48015200-48025200	Weak transcription	Primary T cells from cord blood	blood
27	chr12:48015600-48055200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr12:48016000-48044400	Weak transcription	NH-A	brain
29	chr12:48017000-48024400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:48018000-48036800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr12:48018600-48026000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:48018600-48029000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:48018800-48028400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:48018800-48029000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr12:48018800-48030600	Weak transcription	Fetal Stomach	stomach
36	chr12:48019600-48024200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr12:48019600-48024400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:48020000-48027400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:48020800-48024400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:48020800-48029800	Weak transcription	Fetal Muscle Leg	muscle
41	chr12:48021200-48028200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr12:48022400-48024400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:48022800-48024400	Weak transcription	Adipose Nuclei	Adipose
44	chr12:48022800-48024400	Weak transcription	Fetal Lung	lung
45	chr12:48023000-48030400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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