Variant report

Variant	rs7987608
Chromosome Location	chr13:49222088-49222089
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	chr13:49221601..49222385-chr13:49305871..49306516,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1009719	0.85[ASN][1000 genomes]
rs12050047	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12583212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12583622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12585234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12864882	0.87[ASN][1000 genomes]
rs12865846	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12867110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12867640	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12870838	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12870872	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12871411	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12871822	0.83[ASN][1000 genomes]
rs12876715	0.83[ASN][1000 genomes]
rs1326697	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1359107	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1980838	0.85[ASN][1000 genomes]
rs1980839	0.85[ASN][1000 genomes]
rs2146861	0.85[ASN][1000 genomes]
rs2148516	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34119347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36088391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59136233	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59927903	0.83[ASN][1000 genomes]
rs7331325	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7334400	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7982278	0.93[EUR][1000 genomes]
rs7988330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7989251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535055	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9535056	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9535058	0.87[ASN][1000 genomes]
rs9535061	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9562835	0.94[ASN][1000 genomes]
rs9562836	0.94[ASN][1000 genomes]
rs9562837	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9562838	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9568057	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9568060	0.85[ASN][1000 genomes]
rs9568063	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9568066	0.83[ASN][1000 genomes]
rs9568067	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9568068	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9568070	0.83[ASN][1000 genomes]
rs9568071	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9568072	0.83[ASN][1000 genomes]
rs9568075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568077	0.94[ASN][1000 genomes]
rs9568079	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9634815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9634816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9634817	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9742182	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv832605	chr13:49171305-49344970	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv3495983	chr13:49181790-49222165	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3495984	chr13:49181790-49222165	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv525996	chr13:49210802-49222178	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7987608	CYSLTR2	cis	lymphoblastoid	seeQTL
rs7987608	ITM2B	cis	lymphoblastoid	seeQTL
rs7987608	LRCH1	cis	parietal	SCAN
rs7987608	C13orf18	cis	parietal	SCAN
rs7987608	LPAR6	cis	parietal	SCAN
rs7987608	C13orf1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49220200-49222600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr13:49221400-49226200	Weak transcription	Dnd41	blood
3	chr13:49221600-49223000	Enhancers	Adipose Nuclei	Adipose
4	chr13:49221800-49222600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr13:49222000-49225200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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