Variant report

Variant	rs6042578
Chromosome Location	chr20:1471420-1471421
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10485824	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11087048	1.00[ASN][1000 genomes]
rs11697322	1.00[CHB][hapmap]
rs11697395	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11697973	1.00[ASN][1000 genomes]
rs11697987	1.00[ASN][1000 genomes]
rs11698000	1.00[ASN][1000 genomes]
rs11699494	1.00[CHB][hapmap]
rs13163	1.00[CHB][hapmap]
rs13433171	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16994239	1.00[CHB][hapmap]
rs16994549	1.00[CHB][hapmap]
rs16995146	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16995228	1.00[ASN][1000 genomes]
rs16995310	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16995332	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17793560	1.00[CHB][hapmap]
rs17794135	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1883933	1.00[CHB][hapmap]
rs1884390	1.00[CHB][hapmap]
rs2064645	1.00[CHB][hapmap]
rs2064646	1.00[CHB][hapmap]
rs2249832	1.00[CHB][hapmap]
rs2250091	1.00[CHB][hapmap]
rs2253429	1.00[CHB][hapmap]
rs2253431	1.00[CHB][hapmap]
rs2253693	1.00[CHB][hapmap]
rs2253698	1.00[CHB][hapmap]
rs2256095	1.00[CHB][hapmap]
rs2256229	1.00[CHB][hapmap]
rs2256240	1.00[CHB][hapmap]
rs2256243	1.00[CHB][hapmap]
rs2256250	1.00[CHB][hapmap]
rs2256251	1.00[CHB][hapmap]
rs2263656	1.00[CHB][hapmap]
rs2873522	1.00[CHB][hapmap]
rs33999287	1.00[ASN][1000 genomes]
rs35442028	1.00[ASN][1000 genomes]
rs4536713	1.00[ASN][1000 genomes]
rs45512895	1.00[ASN][1000 genomes]
rs4577347	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4813115	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4814102	1.00[CHB][hapmap]
rs4814391	1.00[CHB][hapmap]
rs56035174	1.00[ASN][1000 genomes]
rs57806058	1.00[ASN][1000 genomes]
rs59377624	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59681252	1.00[ASN][1000 genomes]
rs6033534	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6033554	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6033660	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6033672	1.00[ASN][1000 genomes]
rs6033871	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033896	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033914	1.00[CHB][hapmap]
rs6033935	1.00[CHB][hapmap]
rs6041382	1.00[ASN][1000 genomes]
rs6041689	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6041716	1.00[CHB][hapmap]
rs6041717	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6042000	1.00[ASN][1000 genomes]
rs6042506	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042568	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042585	1.00[CHB][hapmap]
rs6042588	1.00[CHB][hapmap]
rs6042676	1.00[CHB][hapmap]
rs6042689	1.00[CHB][hapmap]
rs6043372	1.00[CHB][hapmap]
rs6043374	1.00[CHB][hapmap]
rs6078575	1.00[CHB][hapmap]
rs6105031	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6105101	1.00[CHB][hapmap]
rs6105437	1.00[CHB][hapmap]
rs6109437	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6109511	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6109522	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6109740	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6109784	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6109984	1.00[CHB][hapmap]
rs6109989	1.00[CHB][hapmap]
rs6110189	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6110193	1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62187542	1.00[ASN][1000 genomes]
rs62187543	1.00[ASN][1000 genomes]
rs62623705	1.00[ASN][1000 genomes]
rs6514337	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6514364	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs715217	1.00[CHB][hapmap]
rs7271240	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7274052	1.00[ASN][1000 genomes]
rs73067251	1.00[ASN][1000 genomes]
rs73069188	1.00[ASN][1000 genomes]
rs73076965	1.00[ASN][1000 genomes]
rs73076966	1.00[ASN][1000 genomes]
rs73579382	1.00[ASN][1000 genomes]
rs73581208	1.00[ASN][1000 genomes]
rs747611	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8117563	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8117744	1.00[ASN][1000 genomes]
rs8118276	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8119259	1.00[ASN][1000 genomes]
rs912113	1.00[CHB][hapmap]
rs958839	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv833893	chr20:1414615-1527779	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1468600-1472400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr20:1469000-1471600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr20:1469200-1473000	Enhancers	HMEC	breast
4	chr20:1469800-1471600	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr20:1469800-1472400	Active TSS	Brain Hippocampus Middle	brain
6	chr20:1469800-1472600	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr20:1469800-1474000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr20:1470000-1471600	Active TSS	Adipose Nuclei	Adipose
9	chr20:1470000-1472600	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr20:1470000-1473200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr20:1470200-1472200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr20:1470200-1472400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr20:1470400-1471600	Active TSS	Primary T cells from cord blood	blood
14	chr20:1470600-1471600	Active TSS	Brain Substantia Nigra	brain
15	chr20:1470600-1471600	Enhancers	NHEK	skin
16	chr20:1470600-1473000	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr20:1470800-1472200	Active TSS	Brain Anterior Caudate	brain
18	chr20:1470800-1472400	Active TSS	Duodenum Mucosa	Duodenum
19	chr20:1471000-1472000	Active TSS	Brain Cingulate Gyrus	brain
20	chr20:1471000-1472000	Active TSS	Colonic Mucosa	Colon
21	chr20:1471000-1472200	Flanking Active TSS	Placenta	Placenta
22	chr20:1471000-1472600	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr20:1471000-1473000	Flanking Active TSS	HUVEC	blood vessel
24	chr20:1471200-1472000	Active TSS	Fetal Muscle Leg	muscle
25	chr20:1471200-1473000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr20:1471400-1471600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr20:1471400-1471800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr20:1471400-1471800	Active TSS	Right Atrium	heart
29	chr20:1471400-1471800	Active TSS	Monocytes-CD14+_RO01746	blood
30	chr20:1471400-1472000	Active TSS	Left Ventricle	heart
31	chr20:1471400-1472000	Enhancers	Lung	lung
32	chr20:1471400-1472400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr20:1471400-1473400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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