Variant report

Variant	rs3743479
Chromosome Location	chr15:77406396-77406397
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77397830..77402873-chr15:77403837..77409871,6	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11072643	0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1125617	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11630689	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11632941	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];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11636648	0.81[JPT][hapmap]
rs11853287	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11853460	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11854193	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11857294	0.84[EUR][1000 genomes]
rs11858641	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes]
rs12443386	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12900433	0.84[ASN][1000 genomes]
rs12901297	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12904088	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907847	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12908262	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12909924	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12913233	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12914128	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12916731	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1446312	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1823100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1867779	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2175941	0.83[EUR][1000 genomes]
rs28584877	0.80[EUR][1000 genomes]
rs3743478	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];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4243045	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	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4886511	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4886849	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4886850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886856	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62008452	0.83[EUR][1000 genomes]
rs7163503	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7169831	0.81[JPT][hapmap]
rs7177533	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8026500	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8028571	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[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	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS 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
3	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
4	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
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3743479	HMG20A	cis	cerebellum	SCAN
rs3743479	HEXA	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77390400-77406400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr15:77394600-77413400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr15:77397600-77411200	Weak transcription	HUVEC	blood vessel
4	chr15:77397800-77411400	Weak transcription	Fetal Thymus	thymus
5	chr15:77398000-77411600	Weak transcription	Fetal Brain Female	brain
6	chr15:77400000-77411400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:77400200-77406400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr15:77400200-77411400	Weak transcription	Stomach Mucosa	stomach
9	chr15:77400200-77424200	Weak transcription	Esophagus	oesophagus
10	chr15:77400200-77427200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr15:77400200-77429000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:77400400-77411400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr15:77400400-77413000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:77400400-77428600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr15:77400600-77406400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:77400600-77406400	Weak transcription	Brain Anterior Caudate	brain
17	chr15:77400600-77406400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr15:77400600-77406600	Weak transcription	Brain Angular Gyrus	brain
19	chr15:77400600-77411400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr15:77400600-77411400	Weak transcription	Brain Substantia Nigra	brain
21	chr15:77400600-77411400	Weak transcription	Small Intestine	intestine
22	chr15:77400600-77425400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr15:77400800-77406400	Weak transcription	Brain Hippocampus Middle	brain
24	chr15:77401000-77411600	Weak transcription	Fetal Kidney	kidney
25	chr15:77401400-77406400	Weak transcription	Ovary	ovary
26	chr15:77401600-77449600	Weak transcription	Colonic Mucosa	Colon
27	chr15:77401800-77411400	Weak transcription	NH-A	brain
28	chr15:77402000-77407600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:77402400-77406400	Weak transcription	Liver	Liver
30	chr15:77402800-77412600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr15:77403000-77407600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr15:77403800-77407400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr15:77404200-77406800	Strong transcription	Fetal Lung	lung
34	chr15:77404200-77407000	Genic enhancers	Fetal Muscle Leg	muscle
35	chr15:77404200-77407400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:77404200-77407400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr15:77404200-77407600	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr15:77404200-77407600	Strong transcription	Fetal Stomach	stomach
39	chr15:77404200-77407800	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr15:77404200-77408200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr15:77404200-77430800	Weak transcription	Thymus	Thymus
42	chr15:77404400-77406400	Weak transcription	Gastric	stomach
43	chr15:77404400-77406400	Enhancers	HSMMtube	muscle
44	chr15:77404400-77409000	Weak transcription	K562	blood
45	chr15:77404600-77406600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:77404600-77406600	Genic enhancers	NHDF-Ad	bronchial
47	chr15:77404600-77411600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr15:77404600-77419200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:77404600-77435600	Weak transcription	HMEC	breast
50	chr15:77404800-77407400	Strong transcription	HepG2	liver

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