Variant report

Variant	rs10506347
Chromosome Location	chr12:57331087-57331088
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57330845..57332526-chr12:57336068..57338551,2	MCF-7	breast:
2	chr12:57323485..57328382-chr12:57328704..57333004,6	K562	blood:
3	chr12:57322265..57324003-chr12:57330480..57332983,2	MCF-7	breast:
4	chr12:57319668..57321739-chr12:57328699..57331375,2	MCF-7	breast:
5	chr12:57328529..57331302-chr12:57397442..57399597,2	K562	blood:
6	chr12:57325326..57326887-chr12:57330449..57332916,2	K562	blood:

Variant related genes	Relation type
ENSG00000170426	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10400412	0.88[AMR][1000 genomes]
rs10400555	0.88[AMR][1000 genomes]
rs10506350	0.91[CEU][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs1072670	0.91[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11172071	0.85[GIH][hapmap]
rs11834851	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs11834856	0.87[EUR][1000 genomes]
rs11836517	0.95[EUR][1000 genomes]
rs12099695	0.84[GIH][hapmap];0.88[AMR][1000 genomes]
rs12810024	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12810837	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12812499	0.89[EUR][1000 genomes]
rs12815538	0.92[EUR][1000 genomes]
rs12818342	0.87[EUR][1000 genomes]
rs12824682	0.87[EUR][1000 genomes]
rs12827039	0.87[EUR][1000 genomes]
rs12827286	0.87[EUR][1000 genomes]
rs1552245	0.83[AMR][1000 genomes]
rs17119301	0.91[CEU][hapmap];0.96[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs17119327	0.88[AMR][1000 genomes]
rs17119330	0.88[AMR][1000 genomes]
rs17119344	0.83[AMR][1000 genomes]
rs17119352	0.83[AMR][1000 genomes]
rs17119386	0.83[AMR][1000 genomes]
rs17119388	0.83[AMR][1000 genomes]
rs17119390	0.83[AMR][1000 genomes]
rs1843311	0.91[EUR][1000 genomes]
rs1843312	0.91[EUR][1000 genomes]
rs1843313	0.91[EUR][1000 genomes]
rs2167306	0.89[EUR][1000 genomes]
rs2270736	0.83[AMR][1000 genomes]
rs2270737	0.81[GIH][hapmap];0.83[AMR][1000 genomes]
rs2279373	0.84[GIH][hapmap];0.86[AMR][1000 genomes]
rs2291855	0.88[AMR][1000 genomes]
rs2371717	0.86[AMR][1000 genomes]
rs28589663	0.87[EUR][1000 genomes]
rs2888139	0.89[EUR][1000 genomes]
rs34186462	0.87[EUR][1000 genomes]
rs34253098	0.89[EUR][1000 genomes]
rs34359134	0.87[EUR][1000 genomes]
rs34969650	0.87[EUR][1000 genomes]
rs35034299	0.87[EUR][1000 genomes]
rs35243318	0.87[EUR][1000 genomes]
rs35493121	0.84[GIH][hapmap];0.88[AMR][1000 genomes]
rs3782329	0.83[AMR][1000 genomes]
rs3782330	0.83[AMR][1000 genomes]
rs3803018	0.88[AMR][1000 genomes]
rs4016338	0.86[AMR][1000 genomes]
rs4143085	0.83[AMR][1000 genomes]
rs56128678	0.83[AMR][1000 genomes]
rs56270558	0.83[AMR][1000 genomes]
rs56354404	0.83[AMR][1000 genomes]
rs57129030	0.87[EUR][1000 genomes]
rs57351760	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57558853	0.88[AMR][1000 genomes]
rs58267004	0.87[AFR][1000 genomes]
rs58298943	0.88[AMR][1000 genomes]
rs60258120	0.87[EUR][1000 genomes]
rs60273384	0.88[AMR][1000 genomes]
rs60380217	0.90[EUR][1000 genomes]
rs61504157	0.83[AMR][1000 genomes]
rs67476535	0.88[AMR][1000 genomes]
rs67771054	0.95[EUR][1000 genomes]
rs67844278	0.86[EUR][1000 genomes]
rs68126184	0.88[AMR][1000 genomes]
rs697222	0.87[GIH][hapmap]
rs7136770	0.91[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs71461303	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72482268	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73114426	0.88[AMR][1000 genomes]
rs73114428	0.88[AMR][1000 genomes]
rs73114434	0.86[AMR][1000 genomes]
rs73114436	0.88[AMR][1000 genomes]
rs73114437	0.88[AMR][1000 genomes]
rs73114446	0.83[AMR][1000 genomes]
rs73114452	0.83[AMR][1000 genomes]
rs73114457	0.83[AMR][1000 genomes]
rs73114459	0.83[AMR][1000 genomes]
rs73114467	0.83[AMR][1000 genomes]
rs73114468	0.83[AMR][1000 genomes]
rs73131120	0.88[AMR][1000 genomes]
rs7314151	0.84[GIH][hapmap]
rs733629	0.88[AMR][1000 genomes]
rs746049	0.91[CEU][hapmap];0.90[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs7487948	0.89[EUR][1000 genomes]
rs754398	0.82[EUR][1000 genomes]
rs755221	0.83[AMR][1000 genomes]
rs7956166	0.89[EUR][1000 genomes]
rs7969312	0.89[EUR][1000 genomes]
rs7972615	0.88[AMR][1000 genomes]
rs901068	0.82[CEU][hapmap];0.90[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv1043846	chr12:57323709-57377509	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10506347	SMAGP	cis	parietal	SCAN
rs10506347	RDH16	cis	cerebellum	SCAN
rs10506347	STAT6	cis	multi-tissue	Pritchard
rs10506347	ZBTB39	cis	parietal	SCAN
rs10506347	OR6C3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57325800-57335200	Weak transcription	Fetal Intestine Large	intestine
2	chr12:57326400-57335200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:57327000-57335200	Weak transcription	Spleen	Spleen
4	chr12:57328200-57335000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:57329400-57335200	Weak transcription	A549	lung
6	chr12:57329800-57335000	Weak transcription	NHEK	skin
7	chr12:57330000-57334600	Weak transcription	HMEC	breast
8	chr12:57330000-57335200	Weak transcription	K562	blood
9	chr12:57330200-57335200	Weak transcription	Esophagus	oesophagus

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