Variant report

Variant	rs17027899
Chromosome Location	chr2:63673231-63673232
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	chr2:63672019..63673524-chr2:63676207..63678360,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10169292	0.80[YRI][hapmap]
rs10180262	1.00[EUR][1000 genomes]
rs10203845	1.00[EUR][1000 genomes]
rs11675647	0.80[YRI][hapmap]
rs12713478	0.80[YRI][hapmap]
rs13431266	0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs1517401	0.89[YRI][hapmap]
rs17027850	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027894	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027897	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027901	0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027902	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027903	0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027904	0.89[YRI][hapmap]
rs17027906	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027922	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027970	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17028098	1.00[EUR][1000 genomes]
rs2030188	0.80[YRI][hapmap]
rs2176416	0.80[YRI][hapmap]
rs2176417	0.80[YRI][hapmap]
rs2421886	0.80[YRI][hapmap]
rs56778186	1.00[EUR][1000 genomes]
rs57272995	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57360299	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57518057	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57702773	1.00[EUR][1000 genomes]
rs57840658	1.00[EUR][1000 genomes]
rs58051386	1.00[EUR][1000 genomes]
rs58523998	1.00[EUR][1000 genomes]
rs58695205	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58718173	1.00[EUR][1000 genomes]
rs59718895	1.00[EUR][1000 genomes]
rs59969247	1.00[EUR][1000 genomes]
rs59973565	1.00[EUR][1000 genomes]
rs60215951	1.00[EUR][1000 genomes]
rs60413056	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60600949	1.00[EUR][1000 genomes]
rs60935023	1.00[EUR][1000 genomes]
rs61165969	1.00[EUR][1000 genomes]
rs61271282	1.00[EUR][1000 genomes]
rs6709115	0.80[YRI][hapmap]
rs6713500	0.80[YRI][hapmap]
rs6717060	0.80[YRI][hapmap]
rs6736411	0.80[YRI][hapmap]
rs932171	0.80[YRI][hapmap]

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	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv1800788	chr2:63473443-63900292	ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv874235	chr2:63622470-63709708	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17027899	SLC6A17	trans	lymphoblastoid	seeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63631800-63675800	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr2:63631800-63677200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:63631800-63681200	Weak transcription	Aorta	Aorta
4	chr2:63631800-63688000	Weak transcription	Right Ventricle	heart
5	chr2:63652600-63673800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr2:63653200-63673800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:63654600-63678200	Weak transcription	Psoas Muscle	Psoas
8	chr2:63655000-63679000	Weak transcription	Primary T cells from cord blood	blood
9	chr2:63656200-63675600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:63657400-63675400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:63658800-63674000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr2:63659200-63679200	Weak transcription	Brain Hippocampus Middle	brain
13	chr2:63659600-63679000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:63661800-63673400	Weak transcription	Fetal Brain Female	brain
15	chr2:63662000-63698000	Weak transcription	Ovary	ovary
16	chr2:63662200-63681400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:63662800-63688000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:63666400-63688000	Weak transcription	Primary B cells from cord blood	blood
19	chr2:63666600-63726800	Weak transcription	Gastric	stomach
20	chr2:63667000-63680600	Weak transcription	Adipose Nuclei	Adipose
21	chr2:63668200-63684800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:63668400-63673400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:63673200-63673600	Genic enhancers	Left Ventricle	heart
24	chr2:63673200-63674600	Weak transcription	Fetal Heart	heart

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