Variant report

Variant	rs9645813
Chromosome Location	chr12:49353138-49353139
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49352012..49353906-chr12:49367184..49368972,2	MCF-7	breast:
2	chr12:49326822..49334011-chr12:49345841..49353556,12	MCF-7	breast:
3	chr12:49348867..49353149-chr12:49362475..49369316,15	MCF-7	breast:
4	chr12:49244315..49247663-chr12:49350223..49353820,7	MCF-7	breast:
5	chr12:49349743..49353633-chr12:49353636..49360057,10	MCF-7	breast:
6	chr12:49351134..49353553-chr12:49353996..49358640,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238395	Chromatin interaction
ENSG00000169884	Chromatin interaction
ENSG00000255863	Chromatin interaction
ENSG00000174243	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1051886	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1054376	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10747556	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10747557	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10747558	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783289	0.82[ASN][1000 genomes]
rs10783293	0.84[ASN][1000 genomes]
rs10783294	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10783295	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10783297	0.92[ASN][1000 genomes]
rs10875886	0.83[ASN][1000 genomes]
rs10875888	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10875893	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10875894	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10875895	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10875896	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10875897	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875898	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875900	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10875901	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10875902	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1111662	0.91[ASN][1000 genomes]
rs11168779	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168783	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168784	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168785	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11168790	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11168792	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11168794	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11168795	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168797	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168798	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168800	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168801	0.97[ASN][1000 genomes]
rs11168803	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168811	0.82[ASN][1000 genomes]
rs11168812	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11608916	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11610459	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11610497	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11614474	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12227240	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12228521	0.83[ASN][1000 genomes]
rs12229275	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12423542	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12579249	0.84[ASN][1000 genomes]
rs1318692	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1690182	0.93[ASN][1000 genomes]
rs1818996	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1830192	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2030900	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2070940	0.93[ASN][1000 genomes]
rs2073480	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2131713	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2272311	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2272312	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2293449	0.85[ASN][1000 genomes]
rs2368701	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2453063	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2463175	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2641450	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2694839	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2694840	0.90[ASN][1000 genomes]
rs3741627	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3759146	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3782353	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3809147	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3825182	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3825184	0.83[ASN][1000 genomes]
rs4018510	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4237854	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4433614	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4526804	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4760600	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4760661	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4760662	0.87[EUR][1000 genomes]
rs4760663	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4760664	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4760665	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4760666	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760667	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760668	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58023472	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59087236	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61941142	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61942166	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61942167	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61942169	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61942207	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61942209	0.83[ASN][1000 genomes]
rs6580696	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7297958	0.84[ASN][1000 genomes]
rs7298330	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7304942	0.84[ASN][1000 genomes]
rs7313988	0.93[ASN][1000 genomes]
rs7489036	0.83[ASN][1000 genomes]
rs7963018	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7963160	0.91[ASN][1000 genomes]
rs7976473	0.86[ASN][1000 genomes]
rs833820	0.91[ASN][1000 genomes]
rs833821	0.91[ASN][1000 genomes]
rs833822	0.93[ASN][1000 genomes]
rs833827	0.93[ASN][1000 genomes]
rs833828	0.91[ASN][1000 genomes]
rs833839	0.83[ASN][1000 genomes]
rs833840	0.83[ASN][1000 genomes]
rs833841	0.82[ASN][1000 genomes]
rs833842	0.82[ASN][1000 genomes]
rs961320	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9783452	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9783477	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9788029	0.85[ASN][1000 genomes]
rs9795742	0.82[ASN][1000 genomes]
rs9796008	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]

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	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9645813	RP11-302B13.1	cis	Whole Blood	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49351800-49358600	Weak transcription	Lung	lung
2	chr12:49351800-49365000	Weak transcription	Right Atrium	heart
3	chr12:49352000-49354400	Weak transcription	HSMMtube	muscle
4	chr12:49352000-49354600	Weak transcription	HSMM	muscle
5	chr12:49352000-49354800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:49352000-49354800	Weak transcription	HUVEC	blood vessel
7	chr12:49352000-49355000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:49352000-49355000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:49352000-49355000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:49352000-49355000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:49352000-49355000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr12:49352000-49355200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr12:49352000-49355200	Weak transcription	NHDF-Ad	bronchial
14	chr12:49352200-49355000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr12:49352200-49355200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:49352200-49355200	Weak transcription	NHEK	skin
17	chr12:49352200-49358400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:49352400-49354800	Weak transcription	Hela-S3	cervix
19	chr12:49352400-49354800	Weak transcription	HMEC	breast
20	chr12:49352400-49355000	Weak transcription	A549	lung
21	chr12:49352600-49353400	Weak transcription	Rectal Mucosa Donor 29	rectum

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