Variant report

Variant	rs4779893
Chromosome Location	chr15:31843974-31843975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 147 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs10519729	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11071179	0.85[JPT][hapmap]
rs11071196	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11071197	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11071199	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11071236	0.84[ASN][1000 genomes]
rs11852462	0.83[ASN][1000 genomes]
rs11852753	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11854065	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11854631	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11856520	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11856610	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11856799	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11857718	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12050678	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12050886	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12050894	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12898638	0.84[ASN][1000 genomes]
rs12898674	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12898981	0.84[ASN][1000 genomes]
rs12899509	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12899987	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12900146	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12900789	0.84[ASN][1000 genomes]
rs12900803	0.84[ASN][1000 genomes]
rs12901904	0.84[ASN][1000 genomes]
rs12906216	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12906386	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12907373	0.84[ASN][1000 genomes]
rs12907512	0.83[ASN][1000 genomes]
rs12907720	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12909072	0.84[ASN][1000 genomes]
rs12909183	0.84[ASN][1000 genomes]
rs12909411	0.84[ASN][1000 genomes]
rs12909737	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12912370	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12913322	0.81[EUR][1000 genomes]
rs12914358	0.84[ASN][1000 genomes]
rs12914768	0.84[ASN][1000 genomes]
rs12915326	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1318733	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13380159	0.82[ASN][1000 genomes]
rs1459199	0.84[ASN][1000 genomes]
rs1542453	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16956867	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16956869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2085667	0.84[ASN][1000 genomes]
rs2100715	0.84[ASN][1000 genomes]
rs2125624	0.84[ASN][1000 genomes]
rs2125625	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2219507	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28413613	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28525283	0.84[ASN][1000 genomes]
rs28573802	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2925	0.82[ASN][1000 genomes]
rs34034041	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34268633	0.80[ASN][1000 genomes]
rs34508606	0.84[ASN][1000 genomes]
rs34522308	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34929828	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34932530	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35176167	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35257316	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35332004	0.93[ASN][1000 genomes]
rs35474662	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35535227	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35732420	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4445857	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4584778	0.81[ASN][1000 genomes]
rs4591098	0.83[ASN][1000 genomes]
rs4594225	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4779542	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4779543	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4779544	0.84[ASN][1000 genomes]
rs4779890	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4779894	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4779895	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4779896	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4779897	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4779898	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4779899	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4779900	0.84[ASN][1000 genomes]
rs4779901	0.84[ASN][1000 genomes]
rs4779903	0.84[ASN][1000 genomes]
rs4779905	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4779907	0.84[ASN][1000 genomes]
rs4779909	0.82[EUR][1000 genomes]
rs57641116	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58975032	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59059557	0.80[ASN][1000 genomes]
rs59597551	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60011586	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60461663	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66863932	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67618202	0.81[ASN][1000 genomes]
rs67932861	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7162339	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7164729	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7165528	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7165706	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7166285	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7167462	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7168828	0.82[ASN][1000 genomes]
rs7169106	0.82[ASN][1000 genomes]
rs7169637	0.83[ASN][1000 genomes]
rs7170060	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7171081	0.84[ASN][1000 genomes]
rs7171868	0.84[ASN][1000 genomes]
rs7176601	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7176844	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7177069	0.83[ASN][1000 genomes]
rs7177083	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7177783	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7178637	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7179569	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7183092	0.81[ASN][1000 genomes]
rs721548	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72726931	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7495305	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7496104	0.81[EUR][1000 genomes]
rs8023393	0.84[ASN][1000 genomes]
rs8023394	0.82[ASN][1000 genomes]
rs8023753	0.84[ASN][1000 genomes]
rs8024958	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8025024	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8029308	0.84[ASN][1000 genomes]
rs8029454	0.84[ASN][1000 genomes]
rs8033168	0.84[ASN][1000 genomes]
rs8035863	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8036502	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8040203	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9672229	0.80[ASN][1000 genomes]
rs9744831	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9806275	0.83[ASN][1000 genomes]
rs983242	0.84[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	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS 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	87 gene(s)	inside rSNPs	diseases
3	nsv1051589	chr15:31728004-31972706	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv542320	chr15:31728004-31972706	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv469633	chr15:31731003-31904613	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv482330	chr15:31731003-31904613	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv903845	chr15:31751664-31939001	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv2422205	chr15:31808878-32375021	Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv2422269	chr15:31808878-32375021	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv2422351	chr15:31808878-32375021	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv2422455	chr15:31808878-32375021	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1045095	chr15:31835044-32439113	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4779893	TRPM1	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31830200-31849400	Weak transcription	Aorta	Aorta
2	chr15:31838200-31854200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:31841000-31848200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr15:31841400-31844000	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr15:31842400-31844400	Genic enhancers	Brain Cingulate Gyrus	brain
6	chr15:31842400-31845200	Strong transcription	Stomach Smooth Muscle	stomach
7	chr15:31842400-31846400	Weak transcription	Brain Substantia Nigra	brain
8	chr15:31842400-31852600	Weak transcription	Colonic Mucosa	Colon
9	chr15:31842600-31846800	Weak transcription	Right Ventricle	heart
10	chr15:31843000-31846200	Weak transcription	Spleen	Spleen
11	chr15:31843200-31850200	Weak transcription	Pancreas	Pancrea
12	chr15:31843400-31846400	Weak transcription	Brain Angular Gyrus	brain
13	chr15:31843400-31846400	Weak transcription	Brain Anterior Caudate	brain
14	chr15:31843600-31846400	Weak transcription	Brain Hippocampus Middle	brain
15	chr15:31843600-31846600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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