Variant report

Variant	rs4243045
Chromosome Location	chr15:77455914-77455915
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11072643	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1125617	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11630689	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[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];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11639314	0.83[ASN][1000 genomes]
rs11853287	0.83[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11853460	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11854193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857294	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11858641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[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];0.97[TSI][hapmap]
rs12443386	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12900433	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12901297	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12904088	0.84[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12907847	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12908262	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12909924	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12913233	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12914128	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12916731	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1446312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[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];0.86[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1867779	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2175941	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
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];0.97[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[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];0.97[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4414462	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4886511	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886849	0.81[EUR][1000 genomes]
rs4886850	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886856	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62008452	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7163503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7177533	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8028571	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4243045	HMG20A	cis	cerebellum	SCAN
rs4243045	HEXA	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77427600-77460600	Weak transcription	Right Ventricle	heart
2	chr15:77434200-77460400	Weak transcription	Fetal Brain Male	brain
3	chr15:77436000-77457800	Weak transcription	Spleen	Spleen
4	chr15:77437000-77471200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr15:77438400-77461000	Weak transcription	NH-A	brain
6	chr15:77438600-77457600	Weak transcription	Gastric	stomach
7	chr15:77438600-77461400	Weak transcription	Aorta	Aorta
8	chr15:77438600-77469000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:77438600-77470800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:77439800-77460600	Weak transcription	HSMMtube	muscle
11	chr15:77444200-77460600	Weak transcription	NHEK	skin
12	chr15:77445200-77461000	Weak transcription	Small Intestine	intestine
13	chr15:77447800-77456000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:77448200-77457400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:77449000-77465200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:77450000-77458000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr15:77450000-77460600	Weak transcription	Left Ventricle	heart
18	chr15:77450400-77471200	Weak transcription	Fetal Muscle Leg	muscle
19	chr15:77450600-77471200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr15:77450800-77471200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr15:77451000-77456200	Weak transcription	Psoas Muscle	Psoas
22	chr15:77451000-77466000	Weak transcription	Brain Substantia Nigra	brain
23	chr15:77451000-77468800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:77451000-77470800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr15:77451000-77470800	Weak transcription	Brain Hippocampus Middle	brain
26	chr15:77451000-77471200	Weak transcription	HSMM	muscle
27	chr15:77451000-77478800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr15:77451200-77460200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr15:77451200-77466000	Weak transcription	Brain Anterior Caudate	brain
30	chr15:77451200-77471800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr15:77451200-77491800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:77451400-77457200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr15:77451400-77471200	Weak transcription	NHDF-Ad	bronchial
34	chr15:77451600-77456200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:77451600-77458000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:77452000-77456200	Enhancers	Primary B cells from cord blood	blood
37	chr15:77452200-77456400	Enhancers	Primary B cells from peripheral blood	blood
38	chr15:77452200-77458400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr15:77452400-77469000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr15:77453000-77460800	Weak transcription	Lung	lung
41	chr15:77453400-77456400	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr15:77453600-77456400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr15:77453600-77457400	Enhancers	Primary T cells from cord blood	blood
44	chr15:77453800-77456000	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr15:77453800-77456200	Weak transcription	Thymus	Thymus
46	chr15:77453800-77456600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr15:77453800-77461800	Weak transcription	Colonic Mucosa	Colon
48	chr15:77454000-77456000	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr15:77454000-77456000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr15:77454000-77456000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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