Variant report

Variant	rs687676
Chromosome Location	chr12:48015488-48015489
allele	C/G
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:
2	chr12:48014490..48017395-chr12:48029451..48031685,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10875666	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875677	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10875682	0.82[EUR][1000 genomes]
rs10875685	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs10875687	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs11168167	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168191	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11168192	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11168193	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11168199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs11168200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs11168203	0.82[EUR][1000 genomes]
rs11168208	0.80[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap]
rs11168215	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs12366410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12367193	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12370643	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1541384	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2240079	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs2240080	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs2283346	0.93[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs3764013	0.94[CHB][hapmap]
rs56011001	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56240307	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs582680	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs583752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs602143	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs604662	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs605499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs611627	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs612773	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61917590	0.83[ASN][1000 genomes]
rs61917591	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61917594	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61917595	0.84[EUR][1000 genomes]
rs622098	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623894	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs630777	0.84[ASN][1000 genomes]
rs632944	0.84[ASN][1000 genomes]
rs634833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs642453	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs644531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs646223	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs652380	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs653136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs658567	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs668968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs671961	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs679789	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7136143	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7136561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7137529	0.83[ASN][1000 genomes]
rs7311663	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7316761	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs739858	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7484827	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs7954502	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7968783	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7969186	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs7976748	0.82[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap]
rs7977786	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs864112	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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
rs687676	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	chr12:48007400-48019800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr12:48007400-48041800	Weak transcription	HSMMtube	muscle
5	chr12:48007400-48044800	Weak transcription	Aorta	Aorta
6	chr12:48007400-48055400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:48007600-48028200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:48007600-48032000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:48007600-48037600	Weak transcription	Left Ventricle	heart
10	chr12:48008400-48017800	Weak transcription	Lung	lung
11	chr12:48008400-48018200	Weak transcription	Thymus	Thymus
12	chr12:48008400-48019200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:48008400-48029000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:48008600-48017600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:48008600-48018600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr12:48008600-48033400	Weak transcription	Pancreas	Pancrea
17	chr12:48008800-48017800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:48009000-48023600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:48009000-48032200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:48009200-48018200	Weak transcription	Fetal Intestine Small	intestine
21	chr12:48009800-48036200	Weak transcription	Ovary	ovary
22	chr12:48010200-48027800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:48011200-48017800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:48011600-48029600	Weak transcription	HSMM	muscle
25	chr12:48012800-48017800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr12:48012800-48024400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:48013000-48016000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr12:48013000-48024400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr12:48013000-48025600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:48013000-48029000	Weak transcription	Primary B cells from cord blood	blood
31	chr12:48013200-48024200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:48013400-48016000	Weak transcription	Brain Angular Gyrus	brain
33	chr12:48013400-48024200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:48013400-48024600	Weak transcription	A549	lung
35	chr12:48013600-48020600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:48014000-48016000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr12:48014000-48017000	Weak transcription	Fetal Intestine Large	intestine
38	chr12:48014000-48017600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr12:48014200-48025400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:48014600-48018000	Weak transcription	Fetal Stomach	stomach
41	chr12:48014600-48029200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:48014800-48020400	Weak transcription	Fetal Muscle Leg	muscle
43	chr12:48014800-48030600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:48015200-48025200	Weak transcription	Primary T cells from cord blood	blood
45	chr12:48015400-48018000	Weak transcription	Primary T cells fromperipheralblood	blood

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