Variant report

Variant	rs12624459
Chromosome Location	chr20:24647725-24647726
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:24631399..24634097-chr20:24646074..24647990,2	MCF-7	breast:
2	chr20:24616131..24617827-chr20:24647064..24649863,2	MCF-7	breast:

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs12624448	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12625030	0.86[JPT][hapmap]
rs13037213	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13039543	0.89[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs13040844	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13040961	0.83[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap]
rs13041031	0.83[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap]
rs13045305	0.83[AMR][1000 genomes]
rs13045365	0.83[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap]
rs2006215	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2006216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2092622	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2223827	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2223828	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2387080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28536086	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34025188	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34219444	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34439537	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34938318	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34988127	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35129087	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35646552	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35737177	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35830266	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs35954840	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36039857	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3746326	0.90[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs3813914	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3813915	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4140548	0.91[ASW][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4140549	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4347916	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4405824	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4513358	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4514953	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56220239	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56227934	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56235927	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58773516	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59954369	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036865	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036866	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036867	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6036869	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6036870	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036871	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036872	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036876	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6036878	0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036880	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6036881	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6049845	0.85[AFR][1000 genomes]
rs6049846	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6049847	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6049849	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6049851	0.86[AFR][1000 genomes]
rs6049853	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6049854	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6049855	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6049856	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6049859	1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6049860	0.95[JPT][hapmap]
rs6049861	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6049863	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6049867	0.93[YRI][hapmap]
rs6049868	0.95[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6049869	0.95[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6049870	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6049871	0.95[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6049872	0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6049873	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6049874	0.95[JPT][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6049875	0.93[YRI][hapmap]
rs6049876	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6049877	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6049878	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6049879	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66630249	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66640525	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66725814	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs729540	0.90[JPT][hapmap]
rs735186	0.90[JPT][hapmap]
rs742806	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs742807	0.95[JPT][hapmap];0.94[MEX][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs742808	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs742809	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs761439	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8117582	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8117680	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8124800	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs880502	0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][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	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3332519	chr20:24535099-24815615	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1061412	chr20:24629468-24887869	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv544216	chr20:24629468-24887869	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv524920	chr20:24639916-24683554	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1061537	chr20:24643869-24683649	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv585744	chr20:24647725-24685440	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12624459	PPY	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24634600-24648800	Weak transcription	Gastric	stomach
2	chr20:24639000-24650400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr20:24639200-24648600	Weak transcription	Spleen	Spleen
4	chr20:24641200-24654000	Weak transcription	Aorta	Aorta
5	chr20:24641400-24649400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr20:24641800-24649800	Weak transcription	Right Ventricle	heart
7	chr20:24643400-24649400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr20:24643400-24661400	Weak transcription	Right Atrium	heart
9	chr20:24645800-24657200	Weak transcription	Brain Anterior Caudate	brain
10	chr20:24646200-24648600	Weak transcription	Fetal Brain Male	brain
11	chr20:24646200-24649400	Weak transcription	Fetal Muscle Leg	muscle
12	chr20:24646400-24650200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr20:24646400-24657200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr20:24646600-24657400	Weak transcription	Brain Substantia Nigra	brain
15	chr20:24646800-24657200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr20:24646800-24657400	Weak transcription	Brain Angular Gyrus	brain
17	chr20:24647600-24653800	Weak transcription	Brain Hippocampus Middle	brain

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