Variant report

Variant	rs12146894
Chromosome Location	chr13:52326477-52326478
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1058141	0.86[ASW][hapmap];0.85[MKK][hapmap]
rs1058142	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1060562	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10676	0.81[MKK][hapmap]
rs12427748	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs12427805	0.86[ASW][hapmap];0.83[MKK][hapmap]
rs12430600	0.86[ASW][hapmap];0.85[MKK][hapmap]
rs1475195	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17069413	0.86[ASW][hapmap];0.81[MKK][hapmap]
rs17075907	0.86[ASN][1000 genomes]
rs17532412	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17532524	1.00[ASN][1000 genomes]
rs17532936	0.99[ASN][1000 genomes]
rs17597215	0.86[ASN][1000 genomes]
rs17597531	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1885854	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2296028	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2296029	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2408491	0.86[ASW][hapmap];0.81[MKK][hapmap]
rs2780461	0.87[JPT][hapmap]
rs2897944	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3908968	1.00[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs41292776	0.97[ASN][1000 genomes]
rs4555048	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs483879	0.87[JPT][hapmap]
rs60757273	1.00[ASN][1000 genomes]
rs73199734	1.00[ASN][1000 genomes]
rs73199746	1.00[ASN][1000 genomes]
rs9316551	0.89[LWK][hapmap]
rs9526783	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9526786	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9526788	1.00[JPT][hapmap]
rs9526793	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9526794	0.99[ASN][1000 genomes]
rs9526795	0.93[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9535714	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9535715	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9535717	1.00[JPT][hapmap]
rs9535722	1.00[JPT][hapmap]
rs9535734	0.92[ASN][1000 genomes]
rs9535735	0.96[ASN][1000 genomes]
rs9535737	0.96[ASN][1000 genomes]
rs9535738	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs9535739	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9535741	0.96[ASN][1000 genomes]
rs9535743	1.00[ASN][1000 genomes]
rs9535744	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9535745	1.00[ASN][1000 genomes]
rs9535746	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9535747	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9535748	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535749	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9535750	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9535751	0.97[ASN][1000 genomes]
rs9535752	0.99[ASN][1000 genomes]
rs9535753	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9535754	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9535755	0.99[ASN][1000 genomes]
rs9535756	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832612	chr13:52176983-52362525	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv455884	chr13:52302630-52405251	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv561644	chr13:52302630-52405251	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv455887	chr13:52318522-52405251	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv561645	chr13:52318522-52405251	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription 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	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12146894	TRIM13	cis	cerebellum	SCAN
rs12146894	WDFY2	cis	multi-tissue	Pritchard
rs12146894	WDFY2	cis	parietal	SCAN
rs12146894	FLJ13639	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52305000-52338200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr13:52306200-52339000	Weak transcription	Fetal Kidney	kidney
3	chr13:52308200-52342800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr13:52308400-52326800	Weak transcription	Hela-S3	cervix
5	chr13:52314200-52326600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr13:52315200-52327000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr13:52315600-52328600	Weak transcription	Brain Germinal Matrix	brain
8	chr13:52315600-52332200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr13:52316200-52332200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr13:52316400-52329400	Weak transcription	Brain Anterior Caudate	brain
11	chr13:52318400-52334200	Weak transcription	Fetal Brain Male	brain
12	chr13:52321000-52329600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr13:52322000-52334400	Weak transcription	Colonic Mucosa	Colon
14	chr13:52322400-52329600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr13:52322600-52326600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr13:52322600-52326600	Weak transcription	Fetal Brain Female	brain
17	chr13:52322600-52326600	Weak transcription	Fetal Lung	lung
18	chr13:52322600-52327200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr13:52322600-52327200	Weak transcription	Spleen	Spleen
20	chr13:52322600-52329000	Weak transcription	Fetal Stomach	stomach
21	chr13:52322600-52329400	Weak transcription	Fetal Intestine Large	intestine
22	chr13:52322600-52330000	Weak transcription	Ovary	ovary
23	chr13:52322600-52330400	Weak transcription	Right Ventricle	heart
24	chr13:52322600-52332400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr13:52322600-52334400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr13:52322600-52337000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr13:52322600-52338200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr13:52322600-52338200	Weak transcription	Stomach Mucosa	stomach
29	chr13:52322600-52342200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr13:52322600-52342200	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr13:52322800-52337600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr13:52322800-52338200	Weak transcription	HUVEC	blood vessel
33	chr13:52323000-52326600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr13:52323000-52327000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr13:52323000-52328400	Weak transcription	GM12878-XiMat	blood
36	chr13:52323000-52330200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr13:52323000-52330400	Weak transcription	Fetal Intestine Small	intestine
38	chr13:52323000-52330600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr13:52323000-52333600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr13:52323000-52336400	Weak transcription	K562	blood
41	chr13:52323000-52336600	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr13:52323000-52337200	Strong transcription	Primary B cells from cord blood	blood
43	chr13:52323000-52343400	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr13:52323200-52326600	Weak transcription	Dnd41	blood
45	chr13:52323200-52326600	Weak transcription	Osteobl	bone
46	chr13:52323200-52327000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr13:52323200-52327400	Strong transcription	NH-A	brain
48	chr13:52323200-52329200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr13:52323200-52330400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr13:52323200-52330400	Weak transcription	Colon Smooth Muscle	Colon

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