Variant report

Variant	rs2350312
Chromosome Location	chr12:29417428-29417429
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10492383	0.82[EUR][1000 genomes]
rs11608616	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11609540	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11610197	0.84[EUR][1000 genomes]
rs11610910	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11611420	0.82[EUR][1000 genomes]
rs11611687	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11612172	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11613628	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11614129	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11614901	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11615636	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12314737	0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs12809077	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12810064	0.84[EUR][1000 genomes]
rs12810315	0.84[EUR][1000 genomes]
rs12811723	0.84[EUR][1000 genomes]
rs12813520	0.82[EUR][1000 genomes]
rs12813789	0.86[EUR][1000 genomes]
rs12813996	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12814180	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12814930	0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12815222	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12816511	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12817163	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12817578	0.85[EUR][1000 genomes]
rs12817825	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12817985	0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12819896	0.84[EUR][1000 genomes]
rs12821498	0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12821559	0.81[EUR][1000 genomes]
rs12821708	0.84[EUR][1000 genomes]
rs12822770	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12823372	0.91[EUR][1000 genomes]
rs12823422	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12823485	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12823903	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12824407	0.84[EUR][1000 genomes]
rs12826064	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12829666	0.84[EUR][1000 genomes]
rs12830274	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12830493	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12830678	0.85[EUR][1000 genomes]
rs12830906	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12831730	0.84[EUR][1000 genomes]
rs12832038	0.85[EUR][1000 genomes]
rs12832263	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16934061	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1988943	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2882377	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34162895	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs35618989	0.82[EUR][1000 genomes]
rs35636563	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36126531	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3764952	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4369447	0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67280216	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67324531	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7134744	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7295387	0.84[EUR][1000 genomes]
rs7299158	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7299635	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7299663	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7308372	0.84[EUR][1000 genomes]
rs7314594	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7961336	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7964254	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7979654	0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][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	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2350312	RP11-996F15.2	cis	lung	GTEx
rs2350312	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx
rs2350312	RP11-996F15.2	cis	Esophagus Mucosa	GTEx
rs2350312	RP11-996F15.2	cis	Esophagus Muscularis	GTEx
rs2350312	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx
rs2350312	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs2350312	RP11-996F15.2	cis	Muscle Skeletal	GTEx
rs2350312	RP11-996F15.2	cis	Thyroid	GTEx
rs2350312	RP11-996F15.2	cis	Artery Tibial	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29408200-29423200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr12:29408200-29425800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:29408400-29424000	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr12:29410000-29421000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:29410000-29425800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:29410000-29426200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:29414000-29423400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:29414200-29422800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:29414400-29434000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:29417200-29465400	Weak transcription	Rectal Mucosa Donor 29	rectum

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