Variant report

Variant	rs12904155
Chromosome Location	chr15:51356728-51356729
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	chr15:51349722..51354201-chr15:51354203..51357915,5	MCF-7	breast:
2	chr15:51348379..51350978-chr15:51356203..51357928,2	K562	blood:

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10450980	0.85[ASN][1000 genomes]
rs10468002	0.85[ASN][1000 genomes]
rs10519289	0.94[JPT][hapmap]
rs11070825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11634895	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs11636974	0.93[JPT][hapmap]
rs11854729	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11855242	0.84[ASN][1000 genomes]
rs11856129	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11857981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12899397	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12899586	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs12900916	0.82[ASN][1000 genomes]
rs12901860	0.81[EUR][1000 genomes]
rs12902196	0.82[EUR][1000 genomes]
rs12906205	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12907367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12909780	0.82[EUR][1000 genomes]
rs12911270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12911715	0.82[ASN][1000 genomes]
rs12913094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12916255	0.94[JPT][hapmap]
rs12916334	0.82[EUR][1000 genomes]
rs1438926	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16953045	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16953046	0.82[ASN][1000 genomes]
rs16964048	1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs16964077	0.85[ASN][1000 genomes]
rs17521467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17521789	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17521919	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17599863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17599974	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1904432	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1912097	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2083254	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2278559	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2306333	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28366661	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28430533	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28642856	0.88[ASN][1000 genomes]
rs28835954	0.85[ASN][1000 genomes]
rs34874493	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35114758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35134521	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35416047	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35439349	0.82[EUR][1000 genomes]
rs35655196	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3759806	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3816717	0.94[JPT][hapmap]
rs3825799	0.94[JPT][hapmap]
rs4134038	0.82[EUR][1000 genomes]
rs4775921	0.84[ASN][1000 genomes]
rs55705440	0.85[ASN][1000 genomes]
rs55972942	0.81[ASN][1000 genomes]
rs56098136	0.85[ASN][1000 genomes]
rs56345002	0.85[ASN][1000 genomes]
rs58661036	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59625951	0.85[ASN][1000 genomes]
rs60281978	0.85[ASN][1000 genomes]
rs6493470	0.94[JPT][hapmap]
rs71426066	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71471522	0.82[EUR][1000 genomes]
rs71471523	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71471584	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71471585	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71471587	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7165920	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7166073	0.93[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs7166600	0.82[EUR][1000 genomes]
rs7170009	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7175024	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7178516	0.82[ASN][1000 genomes]
rs7179084	0.82[ASN][1000 genomes]
rs7179321	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74013148	0.85[ASN][1000 genomes]
rs745258	0.82[JPT][hapmap]
rs8026140	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs8028561	0.82[ASN][1000 genomes]
rs8032236	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8032550	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8032866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8036604	0.93[JPT][hapmap]
rs8040954	0.82[JPT][hapmap]
rs9652426	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers 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	80 gene(s)	inside rSNPs	diseases
4	nsv1038778	chr15:51196641-51356728	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv904214	chr15:51204364-51535192	Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1049644	chr15:51265447-51560445	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv428634	chr15:51299632-51446666	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised 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	39 gene(s)	inside rSNPs	diseases
12	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12904155	LEO1	cis	cerebellum	SCAN
rs12904155	AP4E1	cis	multi-tissue	Pritchard
rs12904155	DUOXA2	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51344600-51384400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr15:51344800-51366800	Weak transcription	Right Ventricle	heart
3	chr15:51345400-51357000	Weak transcription	Colon Smooth Muscle	Colon
4	chr15:51348400-51359000	Weak transcription	Fetal Stomach	stomach
5	chr15:51348400-51360000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr15:51348400-51366400	Weak transcription	Aorta	Aorta
7	chr15:51350400-51356800	Weak transcription	Ovary	ovary
8	chr15:51350400-51358800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:51350400-51358800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr15:51350400-51366600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:51350400-51366800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr15:51350400-51367600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:51350600-51369600	Weak transcription	HUVEC	blood vessel
14	chr15:51350800-51359400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:51352800-51358600	Weak transcription	HSMM	muscle
16	chr15:51353000-51357800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:51353000-51361800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr15:51353000-51362000	Weak transcription	HSMMtube	muscle
19	chr15:51353600-51366800	Weak transcription	Spleen	Spleen

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