Variant report

Variant	rs1208373
Chromosome Location	chr1:169175196-169175197
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	chr1:169171835..169174311-chr1:169174995..169177628,2	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1024340	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1024341	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1028180	1.00[CEU][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs1040501	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1080268	1.00[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11809180	0.82[MEX][hapmap]
rs12084964	0.82[MEX][hapmap]
rs12121994	0.90[JPT][hapmap]
rs12143193	0.90[JPT][hapmap]
rs12145146	0.90[JPT][hapmap]
rs12145226	0.90[JPT][hapmap]
rs12725542	0.81[AMR][1000 genomes]
rs12733001	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs12733626	0.90[JPT][hapmap]
rs12735021	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12735250	0.86[AMR][1000 genomes]
rs12735330	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12736886	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12744668	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12748624	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12751379	1.00[CEU][hapmap]
rs12752953	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs12756556	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12757242	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1320964	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1320966	1.00[CEU][hapmap]
rs1533518	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs1533519	1.00[CEU][hapmap]
rs16828165	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16861997	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs16862051	1.00[CEU][hapmap]
rs16862081	1.00[CEU][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs16862097	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs2012757	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2037249	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs2066001	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs2152980	0.81[AMR][1000 genomes]
rs2154125	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2187963	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2271762	1.00[CEU][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs2300160	0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2420011	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2420015	0.90[JPT][hapmap]
rs2420016	0.90[JPT][hapmap]
rs3213586	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs3213587	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs34032351	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34127028	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34246691	0.96[EUR][1000 genomes]
rs34577710	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34651513	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35232870	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35272114	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35448601	0.86[AMR][1000 genomes]
rs35527028	1.00[CEU][hapmap];0.92[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs36013240	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36040633	1.00[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3753299	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3766033	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs3766034	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs3766072	0.83[AMR][1000 genomes]
rs3766075	1.00[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3766076	0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3766078	0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3766083	1.00[CEU][hapmap]
rs3766084	1.00[CEU][hapmap]
rs3766090	0.90[JPT][hapmap]
rs4140538	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs4140539	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs41442344	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4284298	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57913822	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60378653	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61515530	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6675220	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6686677	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67214318	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67317028	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs68023805	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs718031	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72637226	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72637227	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72637228	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7528751	1.00[CEU][hapmap]
rs7538158	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv831858	chr1:169022383-169179068	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1208373	SLC19A2	cis	lymphoblastoid	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169130400-169195200	Weak transcription	Pancreas	Pancrea
2	chr1:169163600-169184000	Weak transcription	Ovary	ovary
3	chr1:169167200-169176400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:169167800-169186800	Weak transcription	Primary T cells from cord blood	blood
5	chr1:169168000-169183800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:169169600-169175600	Weak transcription	Brain Anterior Caudate	brain
7	chr1:169171600-169184000	Weak transcription	Fetal Intestine Small	intestine
8	chr1:169172000-169176600	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:169172400-169183800	Weak transcription	Brain Germinal Matrix	brain
10	chr1:169172400-169207600	Weak transcription	Esophagus	oesophagus
11	chr1:169172600-169227000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:169173200-169202000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:169173600-169183800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:169174400-169175200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:169175000-169175200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:169175000-169175200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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