Variant report

Variant	rs6940137
Chromosome Location	chr6:114416850-114416851
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:114416682..114419101-chr6:114420825..114422417,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10456889	0.84[ASN][1000 genomes]
rs11153457	0.84[ASN][1000 genomes]
rs11153462	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11153463	0.96[ASN][1000 genomes]
rs1154897	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1154898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11752866	0.84[ASN][1000 genomes]
rs11752970	0.82[ASN][1000 genomes]
rs11756975	0.84[ASN][1000 genomes]
rs11966557	0.84[ASN][1000 genomes]
rs12196433	0.87[ASN][1000 genomes]
rs12199104	0.84[ASN][1000 genomes]
rs12205029	0.84[ASN][1000 genomes]
rs12212081	0.84[ASN][1000 genomes]
rs12661982	0.87[ASN][1000 genomes]
rs12662029	0.87[ASN][1000 genomes]
rs13194478	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13195526	0.84[ASN][1000 genomes]
rs13199435	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13201675	0.84[ASN][1000 genomes]
rs13203308	0.87[ASN][1000 genomes]
rs13203419	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13210690	0.87[ASN][1000 genomes]
rs13214829	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1334901	0.91[CHD][hapmap];0.87[ASN][1000 genomes]
rs1334902	0.87[ASN][1000 genomes]
rs1519685	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1519686	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1519687	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1519688	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17075821	0.91[CHD][hapmap];0.87[ASN][1000 genomes]
rs17075832	0.87[ASN][1000 genomes]
rs17075854	0.87[ASN][1000 genomes]
rs17189832	0.91[CHD][hapmap];0.87[ASN][1000 genomes]
rs17190808	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1879129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1973731	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2292945	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34298844	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35080884	0.84[ASN][1000 genomes]
rs35166510	0.84[ASN][1000 genomes]
rs35275613	0.84[ASN][1000 genomes]
rs35680201	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35877583	0.96[ASN][1000 genomes]
rs35944188	0.84[ASN][1000 genomes]
rs36013742	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3897892	0.84[ASN][1000 genomes]
rs4311539	0.84[ASN][1000 genomes]
rs4371870	0.84[ASN][1000 genomes]
rs4463289	0.84[ASN][1000 genomes]
rs4604299	0.84[ASN][1000 genomes]
rs6568828	0.87[ASN][1000 genomes]
rs6904640	0.87[ASN][1000 genomes]
rs6916558	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6919170	0.96[ASN][1000 genomes]
rs6924016	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6926298	0.87[ASN][1000 genomes]
rs71566758	0.84[ASN][1000 genomes]
rs71566761	0.87[ASN][1000 genomes]
rs7739113	0.87[ASN][1000 genomes]
rs7739597	0.84[ASN][1000 genomes]
rs7742511	0.84[ASN][1000 genomes]
rs7744242	0.87[ASN][1000 genomes]
rs7762446	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7772117	0.96[ASN][1000 genomes]
rs7772231	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs915202	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024062	chr6:114311029-114679557	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6940137	SLC35F1	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114402400-114417800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr6:114409200-114421600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:114411800-114418000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:114413200-114419000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:114413400-114417000	Weak transcription	Brain Angular Gyrus	brain
6	chr6:114413400-114417200	Weak transcription	Brain Anterior Caudate	brain
7	chr6:114414400-114417400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr6:114415000-114417400	Weak transcription	Brain Hippocampus Middle	brain
9	chr6:114415000-114429600	Weak transcription	HepG2	liver
10	chr6:114416200-114417400	Enhancers	Brain Substantia Nigra	brain
11	chr6:114416600-114418800	Weak transcription	HSMM	muscle
12	chr6:114416600-114421400	Weak transcription	HSMMtube	muscle
13	chr6:114416800-114417600	Weak transcription	Brain Cingulate Gyrus	brain

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