Variant report

Variant	rs679789
Chromosome Location	chr12:48011244-48011245
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48010127..48013715-chr12:48014407..48017154,4	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10875666	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875677	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10875685	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs10875687	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs11168167	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168191	0.81[EUR][1000 genomes]
rs11168192	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11168193	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11168199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs11168200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11168208	0.80[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap]
rs11168215	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs12366410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12367193	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12370643	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1541384	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2240079	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs2240080	0.94[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs2283346	0.93[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs3764013	0.94[CHB][hapmap]
rs56011001	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56240307	0.84[EUR][1000 genomes]
rs582680	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs583752	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs602143	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs604662	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs605499	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs611627	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs612773	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61917590	0.81[ASN][1000 genomes]
rs61917591	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61917594	0.83[AMR][1000 genomes]
rs61917595	0.80[EUR][1000 genomes]
rs622098	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs623894	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs630777	0.82[ASN][1000 genomes]
rs632944	0.82[ASN][1000 genomes]
rs634833	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs642453	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs644531	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs646223	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs652380	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs653136	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs658567	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs659836	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs668968	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs671961	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs687676	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7136143	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7136561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs7137529	0.81[ASN][1000 genomes]
rs7311663	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7316761	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs739858	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7484827	0.94[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs7954502	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7968783	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7969186	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs7976748	0.82[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap]
rs7977786	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs864112	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[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
rs679789	ENDOU	cis	Thyroid	GTEx

Chromatin state (count:39 , 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	chr12:48007400-48011400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr12:48007400-48011400	Weak transcription	Primary T cells from cord blood	blood
5	chr12:48007400-48012800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:48007400-48019800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr12:48007400-48041800	Weak transcription	HSMMtube	muscle
8	chr12:48007400-48044800	Weak transcription	Aorta	Aorta
9	chr12:48007400-48055400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:48007600-48028200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:48007600-48032000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:48007600-48037600	Weak transcription	Left Ventricle	heart
13	chr12:48008400-48011800	Weak transcription	Primary B cells from cord blood	blood
14	chr12:48008400-48012400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:48008400-48014200	Weak transcription	Fetal Muscle Leg	muscle
16	chr12:48008400-48017800	Weak transcription	Lung	lung
17	chr12:48008400-48018200	Weak transcription	Thymus	Thymus
18	chr12:48008400-48019200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:48008400-48029000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:48008600-48017600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:48008600-48018600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr12:48008600-48033400	Weak transcription	Pancreas	Pancrea
23	chr12:48008800-48017800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:48009000-48023600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:48009000-48032200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:48009200-48018200	Weak transcription	Fetal Intestine Small	intestine
27	chr12:48009400-48014200	Weak transcription	Osteobl	bone
28	chr12:48009600-48012400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:48009800-48036200	Weak transcription	Ovary	ovary
30	chr12:48010200-48027800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr12:48010600-48014000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:48011000-48012400	Enhancers	Fetal Stomach	stomach
33	chr12:48011000-48013600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:48011200-48011600	Strong transcription	HSMM	muscle
35	chr12:48011200-48013000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:48011200-48013400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:48011200-48013400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr12:48011200-48013400	Strong transcription	A549	lung
39	chr12:48011200-48017800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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