Variant report

Variant	rs6043854
Chromosome Location	chr20:16265770-16265771
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:16264271..16267069-chr20:16272916..16274482,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs12624939	1.00[CHB][hapmap]
rs12625552	1.00[CHB][hapmap]
rs13038209	0.82[CEU][hapmap];0.92[EUR][1000 genomes]
rs13039876	0.85[EUR][1000 genomes]
rs13040354	0.88[EUR][1000 genomes]
rs13040454	0.88[EUR][1000 genomes]
rs13040489	0.85[EUR][1000 genomes]
rs13041027	0.81[EUR][1000 genomes]
rs13042199	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13042286	0.88[EUR][1000 genomes]
rs13043684	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs13044096	0.82[CEU][hapmap]
rs13044167	0.88[EUR][1000 genomes]
rs13044284	0.82[CEU][hapmap]
rs1884604	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1884605	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1884606	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2093004	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2144883	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2144887	1.00[JPT][hapmap]
rs2180442	1.00[CHB][hapmap]
rs2208059	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2328017	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2328018	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2328019	1.00[JPT][hapmap]
rs34009116	0.85[EUR][1000 genomes]
rs34271129	0.85[EUR][1000 genomes]
rs34372607	0.92[EUR][1000 genomes]
rs34543355	0.92[EUR][1000 genomes]
rs34776633	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34822784	0.88[EUR][1000 genomes]
rs34914952	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34990368	0.92[EUR][1000 genomes]
rs35123649	0.92[EUR][1000 genomes]
rs35155900	0.85[EUR][1000 genomes]
rs35193759	0.92[EUR][1000 genomes]
rs35281214	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35291129	0.92[EUR][1000 genomes]
rs35458737	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35583105	0.92[EUR][1000 genomes]
rs35933731	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814469	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6034438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6034439	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6034444	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6034446	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs6034447	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6034460	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6034461	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6034487	1.00[CHB][hapmap]
rs6043852	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6043858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6043863	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6043864	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6043870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6043879	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6043881	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6043882	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6043887	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6043892	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6043954	0.82[CEU][hapmap]
rs6075050	0.85[EUR][1000 genomes]
rs6080243	1.00[JPT][hapmap]
rs6105582	1.00[CHB][hapmap]
rs6105603	1.00[CHB][hapmap]
rs6111016	0.92[ASN][1000 genomes]
rs6111021	0.81[CHD][hapmap]
rs66481149	0.88[EUR][1000 genomes]
rs66752755	0.85[EUR][1000 genomes]
rs66839904	0.88[EUR][1000 genomes]
rs67182398	0.88[EUR][1000 genomes]
rs67199324	0.85[EUR][1000 genomes]
rs7271622	1.00[CHB][hapmap]
rs73112319	0.88[EUR][1000 genomes]
rs8117949	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs8119246	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8122535	1.00[CHB][hapmap]
rs8126093	1.00[CEU][hapmap];0.92[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833930	chr20:16134347-16302763	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6043854	UGT2B17	trans	lymphoblastoid	seeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16242400-16275000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr20:16247600-16290800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr20:16248600-16291400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr20:16248800-16267000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr20:16248800-16272600	Weak transcription	Primary T cells from cord blood	blood
6	chr20:16249000-16272800	Weak transcription	Right Ventricle	heart
7	chr20:16249200-16277400	Weak transcription	Brain Substantia Nigra	brain
8	chr20:16250000-16266800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr20:16252000-16270800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr20:16252000-16289400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr20:16252400-16283000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr20:16253000-16277800	Weak transcription	Brain Angular Gyrus	brain
13	chr20:16253600-16268200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr20:16254000-16278800	Weak transcription	Adipose Nuclei	Adipose
15	chr20:16254000-16281400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr20:16254000-16290800	Weak transcription	Esophagus	oesophagus
17	chr20:16254000-16298400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr20:16254200-16278600	Weak transcription	Pancreas	Pancrea
19	chr20:16254200-16284200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr20:16255400-16283000	Weak transcription	Fetal Lung	lung
21	chr20:16261400-16272800	Weak transcription	Osteobl	bone
22	chr20:16261600-16270800	Weak transcription	HepG2	liver
23	chr20:16262000-16266600	Weak transcription	Thymus	Thymus
24	chr20:16262600-16285400	Weak transcription	Ovary	ovary
25	chr20:16262600-16346200	Weak transcription	Gastric	stomach
26	chr20:16263600-16273200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr20:16263600-16277200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr20:16263800-16265800	Enhancers	Psoas Muscle	Psoas
29	chr20:16264400-16281600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr20:16264600-16284000	Weak transcription	Aorta	Aorta
31	chr20:16264800-16290800	Weak transcription	Lung	lung
32	chr20:16265000-16283800	Weak transcription	Primary B cells from cord blood	blood
33	chr20:16265000-16289000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr20:16265200-16273200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr20:16265200-16281200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr20:16265200-16282600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr20:16265400-16265800	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr20:16265600-16267600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr20:16265600-16268400	Weak transcription	Fetal Muscle Leg	muscle
40	chr20:16265600-16270200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr20:16265600-16280600	Weak transcription	Primary B cells from peripheral blood	blood
42	chr20:16265600-16281400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr20:16265600-16281600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr20:16265600-16282000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr20:16265600-16282000	Weak transcription	Fetal Intestine Small	intestine
46	chr20:16265600-16282800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr20:16265600-16284200	Weak transcription	Left Ventricle	heart

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