Variant report

Variant	rs4773244
Chromosome Location	chr13:111383937-111383938
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:111370419..111377483-chr13:111379803..111385146,6	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1061386	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11618891	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12875067	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1441042	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[JPT][hapmap];0.80[LWK][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1441043	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2119479	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2165418	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3809344	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4771707	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4773240	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4773241	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61971615	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6492302	0.84[EUR][1000 genomes]
rs6492303	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6492304	0.81[EUR][1000 genomes]
rs6492305	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6492306	0.82[EUR][1000 genomes]
rs6492308	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7318291	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7319459	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7330080	0.82[EUR][1000 genomes]
rs7337126	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7338458	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs754599	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7985098	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs7986286	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7991766	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9301475	0.84[YRI][hapmap]
rs9301476	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9515273	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9515274	0.88[EUR][1000 genomes]
rs9521905	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9521909	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9521912	0.87[EUR][1000 genomes]
rs9521913	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9521914	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9521915	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9555724	0.95[CEU][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs9555726	0.84[EUR][1000 genomes]
rs9559863	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9588247	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949634	chr13:111151460-111582996	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
2	nsv1044340	chr13:111234073-111692994	Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
3	nsv1048700	chr13:111265350-111658617	Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
4	esv3440925	chr13:111378000-111406978	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
5	nsv1041716	chr13:111378180-111516489	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv541926	chr13:111378180-111516489	Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4773244	CARS2	cis	parietal	SCAN
rs4773244	CARKD	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111372200-111384200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr13:111372400-111384200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:111378200-111385400	Weak transcription	Spleen	Spleen
4	chr13:111378200-111390800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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