Variant report

Variant	rs28579127
Chromosome Location	chr17:67046847-67046848
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10438703	1.00[JPT][hapmap]
rs10512522	0.92[MKK][hapmap];1.00[EUR][1000 genomes]
rs10512524	1.00[EUR][1000 genomes]
rs10512525	1.00[EUR][1000 genomes]
rs12103660	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12103695	0.82[MKK][hapmap];1.00[EUR][1000 genomes]
rs12103736	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12602396	0.84[MEX][hapmap]
rs13342218	1.00[EUR][1000 genomes]
rs16973430	1.00[EUR][1000 genomes]
rs16973507	1.00[EUR][1000 genomes]
rs16973508	1.00[EUR][1000 genomes]
rs16973511	1.00[EUR][1000 genomes]
rs16973554	1.00[CHB][hapmap];1.00[JPT][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]
rs16973575	1.00[EUR][1000 genomes]
rs2058128	1.00[EUR][1000 genomes]
rs28777976	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28851500	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3863518	1.00[EUR][1000 genomes]
rs4968830	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4968991	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58968107	1.00[EUR][1000 genomes]
rs61744800	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7216483	1.00[EUR][1000 genomes]
rs7216499	1.00[EUR][1000 genomes]
rs7220968	1.00[EUR][1000 genomes]
rs7222660	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72559406	1.00[EUR][1000 genomes]
rs73354278	1.00[EUR][1000 genomes]
rs8065592	1.00[EUR][1000 genomes]
rs8076805	1.00[EUR][1000 genomes]
rs8081075	1.00[EUR][1000 genomes]
rs9889750	1.00[EUR][1000 genomes]
rs9890027	1.00[EUR][1000 genomes]
rs9890160	1.00[EUR][1000 genomes]
rs9890600	1.00[EUR][1000 genomes]
rs9890654	1.00[EUR][1000 genomes]
rs9892453	1.00[EUR][1000 genomes]
rs9893173	0.82[LWK][hapmap];0.86[MKK][hapmap];1.00[EUR][1000 genomes]
rs9894894	1.00[EUR][1000 genomes]
rs9895934	1.00[EUR][1000 genomes]
rs9899675	1.00[EUR][1000 genomes]
rs9899818	0.92[MKK][hapmap];1.00[EUR][1000 genomes]
rs9900211	1.00[EUR][1000 genomes]
rs9901117	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9901228	1.00[EUR][1000 genomes]
rs9902715	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9908650	1.00[EUR][1000 genomes]
rs9910224	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9913052	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9914407	1.00[EUR][1000 genomes]
rs9915531	0.82[LWK][hapmap];0.84[MKK][hapmap];1.00[EUR][1000 genomes]
rs9916254	0.85[LWK][hapmap];0.86[MKK][hapmap];1.00[EUR][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	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv833526	chr17:66980758-67137034	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28579127	SLC16A6	cis	lymphoblastoid	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67039800-67051800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr17:67040400-67047600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr17:67040800-67055600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr17:67041400-67072600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr17:67044000-67047000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr17:67044000-67050200	Enhancers	HepG2	liver
7	chr17:67044200-67047000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr17:67044200-67047000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr17:67044200-67047200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr17:67044200-67047600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr17:67044200-67047600	Weak transcription	Colon Smooth Muscle	Colon
12	chr17:67044200-67047600	Weak transcription	NHLF	lung
13	chr17:67044200-67053400	Weak transcription	Left Ventricle	heart
14	chr17:67044400-67047600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr17:67044400-67051000	Weak transcription	Liver	Liver
16	chr17:67044400-67057200	Weak transcription	Fetal Lung	lung
17	chr17:67044600-67047200	Weak transcription	Adipose Nuclei	Adipose
18	chr17:67044600-67049000	Weak transcription	Right Atrium	heart
19	chr17:67045000-67047000	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr17:67045200-67047200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr17:67045200-67048000	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr17:67046000-67049200	Weak transcription	K562	blood
23	chr17:67046200-67047000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr17:67046200-67047200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr17:67046200-67057000	Weak transcription	HUVEC	blood vessel
26	chr17:67046400-67047000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr17:67046400-67047800	Enhancers	Osteobl	bone
28	chr17:67046400-67048000	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr17:67046600-67052800	Weak transcription	Ovary	ovary
30	chr17:67046800-67047200	Enhancers	NHDF-Ad	bronchial

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