Variant report

No.	Distal block	Cell Line	Cell type
1	chr6:53516671..53518665-chr6:53582679..53584844,2	MCF-7	breast:
2	chr6:53581943..53584631-chr6:53587222..53589336,3	MCF-7	breast:
3	chr6:53357833..53358597-chr6:53583369..53584337,3	K562	blood:
4	chr6:53361794..53363880-chr6:53582795..53585369,2	MCF-7	breast:

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10452610	0.92[ASN][1000 genomes]
rs10948779	0.88[CEU][hapmap];0.89[MEX][hapmap]
rs13220665	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs2745462	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs2820215	0.88[CEU][hapmap]
rs2820216	0.88[CEU][hapmap];0.89[MEX][hapmap]
rs3000997	0.88[CEU][hapmap]
rs3000999	0.87[CEU][hapmap]
rs3001009	0.88[CEU][hapmap]
rs3003493	0.88[CEU][hapmap]
rs34069307	0.92[ASN][1000 genomes]
rs34274914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35360324	0.92[ASN][1000 genomes]
rs35610624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35756855	0.84[AMR][1000 genomes]
rs3813849	0.94[CEU][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs4128134	0.92[ASN][1000 genomes]
rs4236113	0.88[CEU][hapmap]
rs4351263	0.88[CEU][hapmap];0.89[MEX][hapmap]
rs4437470	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4489155	0.94[CEU][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs4715424	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs6458972	0.81[CEU][hapmap];0.89[MEX][hapmap]
rs6899886	0.92[ASN][1000 genomes]
rs6924025	0.80[CEU][hapmap]
rs7759946	0.94[CEU][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs9296721	0.88[CEU][hapmap]
rs9367544	0.88[CEU][hapmap];0.89[MEX][hapmap]
rs9370239	0.88[CEU][hapmap]
rs9382234	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs9395886	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2421836	chr6:53581398-53591120	Bivalent Enhancer Weak transcription Enhancers Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6920831	GSTA1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53582400-53584600	Enhancers	Fetal Intestine Small	intestine
2	chr6:53582600-53588400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr6:53582800-53588400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:53583000-53590800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:53583400-53584400	Enhancers	Duodenum Mucosa	Duodenum
6	chr6:53583400-53584600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:53583800-53584400	Enhancers	Dnd41	blood
8	chr6:53583800-53587600	Weak transcription	Pancreas	Pancrea
9	chr6:53583800-53588600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:53583800-53588800	Weak transcription	Fetal Intestine Large	intestine
11	chr6:53584000-53588400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr6:53584200-53590600	Weak transcription	Fetal Kidney	kidney

Quick Search: