Variant report

Variant	rs6921605
Chromosome Location	chr6:53619575-53619576
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53611367..53614111-chr6:53617026..53619641,3	MCF-7	breast:
2	chr6:53618170..53621877-chr6:53658414..53662232,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137269	Chromatin interaction
ENSG00000227885	Chromatin interaction
ENSG00000228614	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10456672	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10755766	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1076701	0.85[CHB][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap]
rs10948775	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11751003	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11758147	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13216331	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4314499	0.88[AMR][1000 genomes]
rs4345397	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4373352	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4400206	1.00[CEU][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4404762	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4441952	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4457161	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4516937	1.00[CEU][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4563705	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4610551	0.81[AMR][1000 genomes]
rs4712043	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4712044	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4715418	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6903399	0.81[AMR][1000 genomes]
rs6908232	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6911995	0.81[ASN][1000 genomes]
rs6925356	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6934324	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7749273	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7756512	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7763482	1.00[CEU][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7776124	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9357776	0.85[CHB][hapmap]
rs9382232	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9382233	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9382235	0.81[AMR][1000 genomes]
rs9382243	0.87[MEX][hapmap];0.83[TSI][hapmap]
rs9382254	0.83[MEX][hapmap]
rs9395876	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9395878	0.83[TSI][hapmap]
rs9474639	0.90[CEU][hapmap];0.94[EUR][1000 genomes]
rs9474640	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9474641	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9474646	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9474649	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6921605	HMGCLL1	cis	parietal	SCAN
rs6921605	TINAG	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53601600-53638000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr6:53606400-53619600	Weak transcription	Right Atrium	heart
3	chr6:53618200-53630200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:53618800-53635800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:53619400-53633400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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