Variant report

Variant	rs4930715
Chromosome Location	chr12:124042949-124042950
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	chr12:124041024..124043349-chr12:124054707..124057427,2	MCF-7	breast:

Extended variants
information (count: 110 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1060638	1.00[ASN][1000 genomes]
rs11057298	0.86[EUR][1000 genomes]
rs11057302	0.96[EUR][1000 genomes]
rs11057306	0.91[EUR][1000 genomes]
rs11572914	1.00[ASN][1000 genomes]
rs11572916	1.00[ASN][1000 genomes]
rs11572919	1.00[ASN][1000 genomes]
rs11572921	1.00[ASN][1000 genomes]
rs11572928	1.00[ASN][1000 genomes]
rs11572929	1.00[ASN][1000 genomes]
rs11572931	1.00[ASN][1000 genomes]
rs11572961	1.00[ASN][1000 genomes]
rs11572965	1.00[ASN][1000 genomes]
rs11572970	1.00[ASN][1000 genomes]
rs11572992	1.00[ASN][1000 genomes]
rs11573002	1.00[ASN][1000 genomes]
rs11573003	1.00[ASN][1000 genomes]
rs11573005	1.00[ASN][1000 genomes]
rs11610013	0.95[EUR][1000 genomes]
rs11615043	0.80[EUR][1000 genomes]
rs11831129	1.00[ASN][1000 genomes]
rs11834369	0.96[EUR][1000 genomes]
rs11837236	0.96[EUR][1000 genomes]
rs12099981	0.96[EUR][1000 genomes]
rs12099986	0.96[EUR][1000 genomes]
rs1568031	1.00[ASN][1000 genomes]
rs1877365	0.96[EUR][1000 genomes]
rs1913847	1.00[ASN][1000 genomes]
rs2340691	0.96[EUR][1000 genomes]
rs28627432	1.00[ASN][1000 genomes]
rs28668364	1.00[ASN][1000 genomes]
rs28743126	1.00[ASN][1000 genomes]
rs35917561	1.00[ASN][1000 genomes]
rs56816130	1.00[ASN][1000 genomes]
rs57071951	1.00[ASN][1000 genomes]
rs58028686	1.00[ASN][1000 genomes]
rs58507743	1.00[ASN][1000 genomes]
rs58680194	1.00[ASN][1000 genomes]
rs58831452	1.00[ASN][1000 genomes]
rs58904890	1.00[ASN][1000 genomes]
rs59279556	1.00[ASN][1000 genomes]
rs59827616	1.00[ASN][1000 genomes]
rs60422010	1.00[ASN][1000 genomes]
rs60577371	1.00[ASN][1000 genomes]
rs61082817	1.00[ASN][1000 genomes]
rs61678733	0.96[EUR][1000 genomes]
rs6488881	0.99[EUR][1000 genomes]
rs6488885	1.00[ASN][1000 genomes]
rs6488889	1.00[ASN][1000 genomes]
rs7134190	1.00[ASN][1000 genomes]
rs7136101	0.96[EUR][1000 genomes]
rs7301377	0.96[EUR][1000 genomes]
rs7303554	0.96[EUR][1000 genomes]
rs7314792	0.87[AMR][1000 genomes]
rs7316613	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73414262	0.96[EUR][1000 genomes]
rs73414295	1.00[ASN][1000 genomes]
rs73416203	1.00[ASN][1000 genomes]
rs73416204	1.00[ASN][1000 genomes]
rs73416211	1.00[ASN][1000 genomes]
rs73416216	1.00[ASN][1000 genomes]
rs73416277	1.00[ASN][1000 genomes]
rs73416283	1.00[ASN][1000 genomes]
rs73416288	1.00[ASN][1000 genomes]
rs73416298	1.00[ASN][1000 genomes]
rs73416299	1.00[ASN][1000 genomes]
rs73416301	1.00[ASN][1000 genomes]
rs73418103	1.00[ASN][1000 genomes]
rs73418104	1.00[ASN][1000 genomes]
rs73418114	1.00[ASN][1000 genomes]
rs73418125	1.00[ASN][1000 genomes]
rs73418139	1.00[ASN][1000 genomes]
rs73418148	1.00[ASN][1000 genomes]
rs73418153	1.00[ASN][1000 genomes]
rs73418159	1.00[ASN][1000 genomes]
rs73418167	1.00[ASN][1000 genomes]
rs73418174	1.00[ASN][1000 genomes]
rs73418179	1.00[ASN][1000 genomes]
rs73418191	1.00[ASN][1000 genomes]
rs73420303	1.00[ASN][1000 genomes]
rs73420351	1.00[ASN][1000 genomes]
rs73420355	1.00[ASN][1000 genomes]
rs73420358	1.00[ASN][1000 genomes]
rs786428	0.96[EUR][1000 genomes]
rs786429	0.96[EUR][1000 genomes]
rs786431	0.96[EUR][1000 genomes]
rs786432	0.96[EUR][1000 genomes]
rs786433	0.94[EUR][1000 genomes]
rs786434	0.96[EUR][1000 genomes]
rs786435	0.96[EUR][1000 genomes]
rs786437	0.93[EUR][1000 genomes]
rs786438	0.96[EUR][1000 genomes]
rs786439	0.96[EUR][1000 genomes]
rs786450	0.96[EUR][1000 genomes]
rs786455	0.84[EUR][1000 genomes]
rs7954782	0.96[EUR][1000 genomes]
rs7958153	0.96[EUR][1000 genomes]
rs7960812	0.96[EUR][1000 genomes]
rs7965466	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968040	0.94[EUR][1000 genomes]
rs7970545	0.94[EUR][1000 genomes]
rs7971779	0.96[EUR][1000 genomes]
rs952360	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv1042181	chr12:124037400-124152950	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4930715	RP11-486O12.2	cis	Muscle Skeletal	GTEx
rs4930715	DDX55	cis	Thyroid	GTEx
rs4930715	DDX55	cis	lung	GTEx
rs4930715	RP11-486O12.2	cis	Thyroid	GTEx
rs4930715	RP11-486O12.2	cis	Artery Aorta	GTEx
rs4930715	RP11-486O12.2	cis	Esophagus Mucosa	GTEx
rs4930715	RP11-486O12.2	cis	Esophagus Muscularis	GTEx
rs4930715	RP11-486O12.2	cis	Nerve Tibial	GTEx
rs4930715	RP11-486O12.2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124040400-124043600	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr12:124040400-124043800	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr12:124042600-124045000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:124042800-124043000	Enhancers	Primary neutrophils fromperipheralblood	blood

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