Variant report

Variant	rs12913233
Chromosome Location	chr15:77543297-77543298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11072643	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1125617	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11630689	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11632941	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];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11632966	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11636554	0.80[EUR][1000 genomes]
rs11639314	0.92[ASN][1000 genomes]
rs11853287	0.83[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11853460	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11854193	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11857294	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11858641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1191196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs12443386	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12900433	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12904088	0.84[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12907847	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12908262	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12909924	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12914128	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12914345	0.81[ASN][1000 genomes]
rs12916731	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1389436	0.81[ASN][1000 genomes]
rs1446312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1473922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs1493700	0.81[ASN][1000 genomes]
rs1565756	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs1565757	0.81[ASN][1000 genomes]
rs1823100	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1867779	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2175941	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28584877	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34591043	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs3743478	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3743479	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4243045	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4414462	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4886511	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886850	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886856	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886862	0.81[ASN][1000 genomes]
rs4886866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs62008452	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6495237	0.87[ASN][1000 genomes]
rs7163503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7177533	1.00[CEU][hapmap]
rs8024485	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs8028571	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8030074	0.81[ASN][1000 genomes]
rs8037426	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv1832234	chr15:77451350-77694607	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv1041064	chr15:77497903-77631698	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1051744	chr15:77511489-77679160	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1044270	chr15:77534919-77611256	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv542445	chr15:77534919-77611256	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv1830237	chr15:77535785-77694607	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12913233	HMG20A	cis	cerebellum	SCAN
rs12913233	HEXA	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77492400-77544000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr15:77505800-77559400	Weak transcription	Psoas Muscle	Psoas
3	chr15:77508000-77543400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:77517400-77559000	Weak transcription	Ovary	ovary
5	chr15:77517600-77545800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr15:77517800-77544200	Weak transcription	NHLF	lung
7	chr15:77519400-77551800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr15:77519600-77551800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr15:77519800-77557200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:77520200-77578800	Weak transcription	Small Intestine	intestine
11	chr15:77523200-77544000	Weak transcription	Pancreas	Pancrea
12	chr15:77526400-77547600	Weak transcription	Liver	Liver
13	chr15:77527000-77559000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:77527000-77576200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr15:77528200-77544200	Weak transcription	NH-A	brain
16	chr15:77528400-77553000	Weak transcription	Aorta	Aorta
17	chr15:77528600-77544000	Weak transcription	Placenta	Placenta
18	chr15:77528800-77559200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:77528800-77571400	Weak transcription	Right Ventricle	heart
20	chr15:77528800-77574400	Weak transcription	HepG2	liver
21	chr15:77528800-77577200	Weak transcription	Spleen	Spleen
22	chr15:77528800-77579200	Weak transcription	Brain Angular Gyrus	brain
23	chr15:77529000-77543800	Weak transcription	HSMMtube	muscle
24	chr15:77529000-77544200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr15:77529000-77544200	Weak transcription	Primary B cells from peripheral blood	blood
26	chr15:77529000-77548600	Weak transcription	Gastric	stomach
27	chr15:77529200-77544000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr15:77529200-77544000	Weak transcription	Fetal Lung	lung
29	chr15:77529200-77545800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr15:77529200-77546400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr15:77529200-77546800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr15:77529200-77561400	Weak transcription	Primary T cells from cord blood	blood
33	chr15:77529400-77544000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr15:77529400-77544200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr15:77529400-77547800	Weak transcription	GM12878-XiMat	blood
36	chr15:77529400-77551800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr15:77529400-77552600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:77529400-77558600	Weak transcription	Fetal Muscle Leg	muscle
39	chr15:77529400-77558600	Weak transcription	Lung	lung
40	chr15:77529400-77558800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr15:77529400-77559000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr15:77529400-77559600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr15:77529400-77565400	Weak transcription	Dnd41	blood
44	chr15:77529400-77574400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr15:77529600-77544200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr15:77532200-77544200	Weak transcription	Primary B cells from cord blood	blood
47	chr15:77534400-77544000	Weak transcription	Hela-S3	cervix
48	chr15:77534600-77545600	Weak transcription	K562	blood
49	chr15:77535000-77545200	Weak transcription	Esophagus	oesophagus
50	chr15:77536000-77543800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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