Variant report

Variant	rs11721460
Chromosome Location	chr4:173940388-173940389
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	chr4:173940054..173943787-chr4:174088159..174091166,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245213	Chromatin interaction
ENSG00000109586	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10019310	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10020676	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs11132976	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11722826	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11939508	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13125629	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13145272	0.90[EUR][1000 genomes]
rs17059107	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28451718	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28569824	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3905287	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4331761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4557236	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4695821	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62341925	0.93[ASN][1000 genomes]
rs6832095	0.92[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6833557	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7669563	0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[EUR][1000 genomes]
rs7680255	0.86[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9996247	0.86[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	nsv948856	chr4:173388217-173967546	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv949126	chr4:173466221-174051451	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11721460	GALNT7	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:173920600-173942400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:173936000-173941000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:173936400-173945000	Weak transcription	HSMM	muscle
4	chr4:173936600-173942400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:173937400-173941000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr4:173937600-173942400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr4:173937600-173944200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:173938800-173940800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:173939200-173940800	Weak transcription	H9 Cell Line	embryonic stem cell

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