Variant report

Variant	rs4729516
Chromosome Location	chr7:98745679-98745680
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:98745667-98745682	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:98740342..98743513-chr7:98744665..98747630,5	MCF-7	breast:
2	chr7:98744404..98747208-chr7:98758596..98760579,2	MCF-7	breast:
3	chr7:98739425..98742547-chr7:98743617..98746560,5	K562	blood:
4	chr7:98738148..98740026-chr7:98743359..98745839,2	MCF-7	breast:
5	chr7:98738526..98746153-chr7:98804876..98809686,18	MCF-7	breast:
6	chr7:98725984..98728681-chr7:98745631..98748345,2	MCF-7	breast:
7	chr7:98741722..98743418-chr7:98744692..98747371,2	MCF-7	breast:
8	chr7:98744627..98747517-chr7:98820164..98821746,2	MCF-7	breast:

No data

Variant related genes	Relation type
SMURF1	TF binding region
ENSG00000198742	Chromatin interaction
ENSG00000185467	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10808110	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10953281	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10953282	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10953283	0.92[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs11982330	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12705030	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12705031	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13222381	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs13235218	0.87[EUR][1000 genomes]
rs17147666	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs2056659	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs34344936	0.87[EUR][1000 genomes]
rs4729515	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4729521	0.92[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs56072276	0.90[EUR][1000 genomes]
rs56132062	0.81[EUR][1000 genomes]
rs62473049	0.90[EUR][1000 genomes]
rs6952161	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6956695	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6965158	0.82[EUR][1000 genomes]
rs7794690	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7807000	0.85[ASN][1000 genomes]
rs941001	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024529	chr7:98194830-98793518	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv539036	chr7:98194830-98793518	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv2755119	chr7:98721885-98800145	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
4	esv1792421	chr7:98737119-98752081	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4729516	SMURF1	cis	parietal	SCAN
rs4729516	TRRAP	cis	cerebellum	SCAN
rs4729516	MUC17	cis	cerebellum	SCAN
rs4729516	PILRB	cis	parietal	SCAN
rs4729516	GATS	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98744000-98745800	Weak transcription	K562	blood

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