Variant report

Variant	rs2146202
Chromosome Location	chr1:168986492-168986493
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:168973185..168974998-chr1:168985373..168988197,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10919009	1.00[ASN][1000 genomes]
rs12075363	1.00[ASN][1000 genomes]
rs12084554	1.00[CHD][hapmap]
rs12122542	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12122546	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12143802	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1320973	1.00[LWK][hapmap]
rs1322486	0.93[CEU][hapmap]
rs1322495	1.00[ASN][1000 genomes]
rs1322502	1.00[ASN][1000 genomes]
rs1322503	1.00[ASN][1000 genomes]
rs1358949	1.00[ASN][1000 genomes]
rs1407479	1.00[ASN][1000 genomes]
rs1570332	1.00[ASN][1000 genomes]
rs1570333	1.00[ASN][1000 genomes]
rs1590286	1.00[ASN][1000 genomes]
rs17349439	1.00[CHD][hapmap]
rs200577	1.00[ASN][1000 genomes]
rs2065130	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2065131	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146195	0.93[CEU][hapmap];1.00[CHD][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap]
rs2146199	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146203	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2419389	1.00[ASN][1000 genomes]
rs2419396	1.00[ASN][1000 genomes]
rs2419685	1.00[ASN][1000 genomes]
rs2900886	1.00[ASN][1000 genomes]
rs2984603	1.00[ASN][1000 genomes]
rs2984605	1.00[ASN][1000 genomes]
rs2984606	1.00[ASN][1000 genomes]
rs2984608	1.00[ASN][1000 genomes]
rs2984609	1.00[ASN][1000 genomes]
rs2984610	1.00[ASN][1000 genomes]
rs2984612	1.00[ASN][1000 genomes]
rs3007379	1.00[CEU][hapmap]
rs3007391	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007394	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3007395	0.87[EUR][1000 genomes]
rs3007396	0.82[EUR][1000 genomes]
rs3007398	1.00[ASN][1000 genomes]
rs3007399	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3007400	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4656168	1.00[ASN][1000 genomes]
rs61801631	1.00[ASN][1000 genomes]
rs61801632	1.00[ASN][1000 genomes]
rs61801637	1.00[ASN][1000 genomes]
rs61801655	1.00[ASN][1000 genomes]
rs61801656	1.00[ASN][1000 genomes]
rs6427154	1.00[ASN][1000 genomes]
rs6670610	1.00[ASN][1000 genomes]
rs6681955	1.00[ASN][1000 genomes]
rs6686910	1.00[ASN][1000 genomes]
rs704837	1.00[ASN][1000 genomes]
rs7513128	1.00[ASN][1000 genomes]
rs7526462	1.00[CHD][hapmap]
rs7541615	1.00[ASN][1000 genomes]
rs857632	1.00[ASN][1000 genomes]
rs857634	1.00[ASN][1000 genomes]
rs857636	1.00[ASN][1000 genomes]
rs857638	1.00[ASN][1000 genomes]
rs857639	1.00[ASN][1000 genomes]
rs857640	1.00[ASN][1000 genomes]
rs857642	1.00[ASN][1000 genomes]
rs857644	1.00[ASN][1000 genomes]
rs911892	1.00[ASN][1000 genomes]
rs968047	1.00[ASN][1000 genomes]
rs971411	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	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2146202	SLC19A2	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168980400-168987000	Weak transcription	Fetal Intestine Small	intestine
2	chr1:168983200-168988600	Weak transcription	GM12878-XiMat	blood
3	chr1:168985400-168989000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:168985400-168989400	Enhancers	Stomach Mucosa	stomach
5	chr1:168985800-168988200	Enhancers	Duodenum Mucosa	Duodenum
6	chr1:168986000-168987000	Weak transcription	Small Intestine	intestine
7	chr1:168986400-168986800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:168986400-168988000	Weak transcription	Gastric	stomach

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