Variant report

Variant	rs2346397
Chromosome Location	chr22:28886805-28886806
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	chr22:28396428..28399039-chr22:28886798..28889695,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1125250	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.90[ASN][1000 genomes]
rs1303845	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs134489	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[MKK][hapmap]
rs134500	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs134507	0.92[JPT][hapmap]
rs134522	0.84[CEU][hapmap]
rs134526	0.91[ASN][1000 genomes]
rs134529	0.80[CEU][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes]
rs134530	0.83[AMR][1000 genomes]
rs134541	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs134543	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs134545	0.84[CEU][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes]
rs134548	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs134551	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2145161	0.80[CEU][hapmap]
rs2346867	0.90[ASN][1000 genomes]
rs34593692	0.86[ASN][1000 genomes]
rs5752743	0.85[JPT][hapmap]
rs5762660	0.85[JPT][hapmap]
rs5762665	0.87[AMR][1000 genomes]
rs5762670	0.81[CEU][hapmap]
rs5762730	0.80[CEU][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap]
rs6005790	0.84[CEU][hapmap]
rs6005835	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs695272	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs695318	0.80[CEU][hapmap]
rs695439	0.99[ASN][1000 genomes]
rs695567	0.84[CEU][hapmap]
rs695591	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs695625	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.95[ASN][1000 genomes]
rs695659	0.92[ASN][1000 genomes]
rs695700	0.84[CEU][hapmap]
rs695762	0.94[ASN][1000 genomes]
rs695796	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs695797	0.97[ASN][1000 genomes]
rs737622	0.81[CEU][hapmap]

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	nsv1067544	chr22:28755418-29055246	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv544674	chr22:28755418-29055246	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv588880	chr22:28807277-29001789	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2346397	TTC28	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28881000-28893400	Weak transcription	NHDF-Ad	bronchial
2	chr22:28882000-28890200	Weak transcription	Left Ventricle	heart
3	chr22:28886800-28887200	ZNF genes & repeats	Dnd41	blood

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