Variant report

Variant	rs13091924
Chromosome Location	chr3:195051136-195051137
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10804414	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1094677	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1105165	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs11706264	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12695049	0.84[ASN][1000 genomes]
rs13059843	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072826	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13072883	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13099106	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13324903	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1538767	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2791603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4677834	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4677835	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55672262	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55927338	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778719	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6785964	0.80[ASN][1000 genomes]
rs7611238	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7633265	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7634345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651757	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs823300	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs823301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs823302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs823306	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs823310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs823311	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs823314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs931528	0.83[CHB][hapmap]
rs9810077	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9823964	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9840346	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
3	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
4	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
5	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer 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
9	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
10	nsv432508	chr3:194916131-195478861	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
11	nsv432510	chr3:194935314-195478861	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
12	nsv1005519	chr3:194964301-195340515	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
13	nsv432511	chr3:194986167-195479748	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
14	nsv432512	chr3:195007260-195475989	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
15	nsv526569	chr3:195038287-195123495	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13091924	ACAP2	cis	cerebellum	SCAN
rs13091924	RPL35A	cis	cerebellum	SCAN
rs13091924	XXYLT1	cis	Esophagus Mucosa	GTEx
rs13091924	ACAP2	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194992600-195090000	Weak transcription	Aorta	Aorta
2	chr3:194993000-195076000	Weak transcription	Fetal Heart	heart
3	chr3:195004000-195066600	Weak transcription	Small Intestine	intestine
4	chr3:195010000-195061000	Weak transcription	Fetal Kidney	kidney
5	chr3:195010000-195076400	Weak transcription	Brain Angular Gyrus	brain
6	chr3:195022600-195073400	Weak transcription	HMEC	breast
7	chr3:195022800-195073400	Weak transcription	NHEK	skin
8	chr3:195026800-195051400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:195034800-195076800	Weak transcription	Psoas Muscle	Psoas
10	chr3:195040400-195051400	Weak transcription	NH-A	brain
11	chr3:195040400-195051800	Weak transcription	Right Ventricle	heart
12	chr3:195040400-195053000	Weak transcription	A549	lung
13	chr3:195040400-195062600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:195040400-195064800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:195040400-195066000	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr3:195040400-195076400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:195040400-195076600	Weak transcription	Brain Anterior Caudate	brain
18	chr3:195040400-195079400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr3:195040400-195108400	Weak transcription	Colonic Mucosa	Colon
20	chr3:195040600-195051200	Weak transcription	HepG2	liver
21	chr3:195040600-195059000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:195040600-195111200	Weak transcription	Fetal Brain Male	brain
23	chr3:195040800-195051600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:195040800-195071200	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr3:195040800-195072800	Weak transcription	K562	blood
26	chr3:195040800-195073200	Weak transcription	Pancreas	Pancrea
27	chr3:195040800-195076400	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:195041000-195051400	Weak transcription	Esophagus	oesophagus
29	chr3:195041000-195051400	Weak transcription	Fetal Muscle Leg	muscle
30	chr3:195041000-195051400	Weak transcription	Left Ventricle	heart
31	chr3:195041000-195051400	Weak transcription	Thymus	Thymus
32	chr3:195041000-195052000	Weak transcription	Fetal Intestine Small	intestine
33	chr3:195041000-195052600	Weak transcription	Fetal Stomach	stomach
34	chr3:195041000-195058400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:195041000-195058400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:195041000-195058600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:195041000-195062600	Weak transcription	Brain Germinal Matrix	brain
38	chr3:195041000-195065400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr3:195041000-195066400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:195041000-195067200	Weak transcription	Brain Substantia Nigra	brain
41	chr3:195041000-195077000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr3:195041000-195131200	Weak transcription	Gastric	stomach
43	chr3:195041200-195077200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr3:195041400-195064800	Strong transcription	Primary B cells from cord blood	blood
45	chr3:195041400-195076800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr3:195041600-195051200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:195041600-195054800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:195041600-195058600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:195041600-195061200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:195041600-195062200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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