Variant report

Variant	rs622098
Chromosome Location	chr12:48007475-48007476
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10875666	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875677	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10875682	0.84[EUR][1000 genomes]
rs10875685	0.83[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap]
rs10875687	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs11168167	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168191	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11168192	0.92[CEU][hapmap];0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11168193	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11168199	0.92[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes]
rs11168200	0.91[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs11168203	0.84[EUR][1000 genomes]
rs11168208	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs11168215	0.88[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap]
rs12366410	0.82[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12367193	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12370643	0.94[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs1541384	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2240079	0.88[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap]
rs2240080	0.88[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap]
rs2283346	0.85[CEU][hapmap];0.88[CHB][hapmap]
rs3764013	0.88[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.80[MKK][hapmap]
rs56011001	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56240307	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs582680	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs583752	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs602143	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs604662	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs605499	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs611627	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs612773	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61917590	0.83[ASN][1000 genomes]
rs61917591	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61917594	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61917595	0.86[EUR][1000 genomes]
rs623894	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs630777	0.84[ASN][1000 genomes]
rs632944	0.84[ASN][1000 genomes]
rs634833	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs642453	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs644531	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs646223	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs652380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs653136	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs658567	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659836	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs668968	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs671961	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs679789	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs687676	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136143	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7136561	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs7137529	0.83[ASN][1000 genomes]
rs7311663	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs7316761	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs739858	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7484827	0.88[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap]
rs7954502	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7968783	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7969186	0.83[CHB][hapmap]
rs7976748	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs7977786	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs864112	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv1051131	chr12:47883981-48016556	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv899056	chr12:47940764-48012390	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv558788	chr12:47945797-48012390	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	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
10	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
11	nsv899057	chr12:47947551-48012390	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	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
13	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs622098	ENDOU	cis	Thyroid	GTEx

Chromatin state (count:25 , 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	chr12:48005800-48008400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:48006000-48007600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:48006000-48008600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
5	chr12:48006200-48009000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:48006400-48007600	ZNF genes & repeats	Primary B cells from cord blood	blood
7	chr12:48006600-48008000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:48006800-48007600	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:48006800-48008000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:48006800-48008400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:48006800-48008400	ZNF genes & repeats	A549	lung
12	chr12:48006800-48008600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:48006800-48009000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
14	chr12:48006800-48009600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:48007200-48011000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:48007200-48024600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:48007400-48008400	Weak transcription	Fetal Lung	lung
18	chr12:48007400-48011200	Weak transcription	HSMM	muscle
19	chr12:48007400-48011400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:48007400-48011400	Weak transcription	Primary T cells from cord blood	blood
21	chr12:48007400-48012800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:48007400-48019800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr12:48007400-48041800	Weak transcription	HSMMtube	muscle
24	chr12:48007400-48044800	Weak transcription	Aorta	Aorta
25	chr12:48007400-48055400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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