Variant report

Variant	rs399484
Chromosome Location	chr3:50589455-50589456
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:50554289..50557093-chr3:50587538..50590064,2	K562	blood:
2	chr3:50407329..50410054-chr3:50589199..50591435,2	K562	blood:
3	chr3:50587657..50590560-chr3:50595008..50597465,2	MCF-7	breast:
4	chr3:50588800..50589787-chr3:50651201..50652268,5	MCF-7	breast:
5	chr3:50473196..50473698-chr3:50588986..50589944,2	K562	blood:
6	chr3:50586399..50591329-chr3:50605671..50609756,8	MCF-7	breast:
7	chr3:50588702..50590001-chr3:50651049..50652105,9	MCF-7	breast:
8	chr3:50376883..50379667-chr3:50587789..50590595,2	K562	blood:
9	chr3:50256257..50258599-chr3:50587633..50590520,2	K562	blood:
10	chr3:50588406..50590999-chr3:50644640..50646722,2	MCF-7	breast:
11	chr3:50478507..50481167-chr3:50588405..50590760,2	K562	blood:
12	chr3:50578851..50581220-chr3:50589353..50591670,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000068028	Chromatin interaction
ENSG00000114735	Chromatin interaction
ENSG00000235058	Chromatin interaction
ENSG00000088543	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1034405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130252	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130255	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs11710858	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11719998	0.81[EUR][1000 genomes]
rs12491425	0.82[EUR][1000 genomes]
rs12639126	0.80[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs129310	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs13076850	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13083004	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084476	0.90[EUR][1000 genomes]
rs13091933	0.94[CEU][hapmap];0.90[CHD][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs13094336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094785	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs13096264	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1458386	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs1458387	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1463496	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1463497	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs175634	0.94[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs17787569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1824280	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs201193	0.82[EUR][1000 genomes]
rs201194	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs201196	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs201197	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs201198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2125366	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2125369	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2168866	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs2227280	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232248	1.00[CEU][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs2232253	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2269505	1.00[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs2269507	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2355321	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2355323	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2609036	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2675810	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs2883652	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs34202063	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34267788	0.87[EUR][1000 genomes]
rs34399912	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34434811	0.87[EUR][1000 genomes]
rs34584636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34756253	0.90[EUR][1000 genomes]
rs34762184	0.89[CHD][hapmap]
rs34889917	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35655236	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35690191	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35714264	0.92[EUR][1000 genomes]
rs35864641	0.87[EUR][1000 genomes]
rs3804627	1.00[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs3804628	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs391620	0.83[EUR][1000 genomes]
rs398703	0.82[EUR][1000 genomes]
rs399971	0.84[EUR][1000 genomes]
rs417592	1.00[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs441516	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4429624	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs443030	0.85[EUR][1000 genomes]
rs4533647	0.87[EUR][1000 genomes]
rs453570	1.00[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs4688702	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs490634	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59949730	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622502	0.84[EUR][1000 genomes]
rs628081	0.94[CEU][hapmap]
rs6446214	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs67425923	0.82[EUR][1000 genomes]
rs67588094	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768300	0.83[EUR][1000 genomes]
rs6775012	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6778680	0.82[CEU][hapmap]
rs67813889	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784166	0.92[EUR][1000 genomes]
rs6787521	1.00[CEU][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6791880	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs695170	0.86[EUR][1000 genomes]
rs71326937	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73082948	0.85[EUR][1000 genomes]
rs750453	0.81[EUR][1000 genomes]
rs750510	0.89[CEU][hapmap]
rs7611428	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs7629253	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs7646236	1.00[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs7650574	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7652715	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs809451	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes]
rs809454	0.82[EUR][1000 genomes]
rs936405	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs936406	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs9830920	0.88[EUR][1000 genomes]
rs9839684	1.00[CHB][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
4	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv460532	chr3:50536273-50616049	Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv590272	chr3:50536273-50616049	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
14	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs399484	CAMP	cis	cerebellum	SCAN
rs399484	APEH	cis	cerebellum	SCAN
rs399484	HEMK1	cis	Esophagus Muscularis	GTEx
rs399484	MAPKAPK3	cis	multi-tissue	Pritchard

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50578600-50595800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:50583600-50603400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:50584400-50592400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:50586000-50597200	Weak transcription	Right Atrium	heart
5	chr3:50586800-50590000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr3:50586800-50590400	Enhancers	Fetal Muscle Leg	muscle
7	chr3:50587000-50589800	Enhancers	Fetal Stomach	stomach
8	chr3:50587200-50592800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:50587600-50592600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:50587600-50603800	Weak transcription	Brain Anterior Caudate	brain
11	chr3:50587800-50589800	Enhancers	Fetal Intestine Small	intestine
12	chr3:50588000-50589600	Enhancers	Fetal Lung	lung
13	chr3:50588000-50590000	Enhancers	Fetal Heart	heart
14	chr3:50588000-50591800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:50588200-50589600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:50588400-50603600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:50589000-50589800	Weak transcription	HMEC	breast

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