Variant report

Variant	rs17027903
Chromosome Location	chr2:63673994-63673995
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr2:63673711-63674043	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:63664087..63666512-chr2:63673273..63675449,2	MCF-7	breast:

Variant related genes	Relation type
WDPCP	TF binding region
ENSG00000143951	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10180262	1.00[EUR][1000 genomes]
rs10203845	1.00[EUR][1000 genomes]
rs13431266	1.00[EUR][1000 genomes]
rs17027850	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027873	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027899	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]
rs17027901	1.00[ASW][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]
rs17027902	0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027904	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs17027906	0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027922	0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];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]
rs56778186	1.00[EUR][1000 genomes]
rs57272995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57360299	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57518057	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57702773	1.00[EUR][1000 genomes]
rs57840658	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58051386	1.00[EUR][1000 genomes]
rs58523998	1.00[EUR][1000 genomes]
rs58695205	0.92[AFR][1000 genomes];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[AFR][1000 genomes];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]
rs6736411	0.90[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
rs17027903	SLC6A17	trans	lymphoblastoid	seeQTL

Chromatin state (count:25 , 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	chr2:63654600-63678200	Weak transcription	Psoas Muscle	Psoas
6	chr2:63655000-63679000	Weak transcription	Primary T cells from cord blood	blood
7	chr2:63656200-63675600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:63657400-63675400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:63658800-63674000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:63659200-63679200	Weak transcription	Brain Hippocampus Middle	brain
11	chr2:63659600-63679000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr2:63662000-63698000	Weak transcription	Ovary	ovary
13	chr2:63662200-63681400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:63662800-63688000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:63666400-63688000	Weak transcription	Primary B cells from cord blood	blood
16	chr2:63666600-63726800	Weak transcription	Gastric	stomach
17	chr2:63667000-63680600	Weak transcription	Adipose Nuclei	Adipose
18	chr2:63668200-63684800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:63673200-63674600	Weak transcription	Fetal Heart	heart
20	chr2:63673400-63674000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:63673600-63697800	Weak transcription	Left Ventricle	heart
22	chr2:63673800-63674000	Active TSS	Primary hematopoietic stem cells	blood
23	chr2:63673800-63674200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:63673800-63674400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:63673800-63674400	Enhancers	NHEK	skin

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