Variant report

Variant	rs4338381
Chromosome Location	chr1:103572927-103572928
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1012282	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10493986	0.83[MEX][hapmap]
rs10493988	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10493991	1.00[JPT][hapmap]
rs10747437	0.92[ASN][1000 genomes]
rs10782921	1.00[JPT][hapmap]
rs10874665	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10874668	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10874677	0.92[ASN][1000 genomes]
rs10874678	0.96[ASN][1000 genomes]
rs10874679	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11164648	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164649	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164653	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11164657	0.80[ASN][1000 genomes]
rs11164658	1.00[JPT][hapmap]
rs11164662	0.88[CHB][hapmap];0.94[ASN][1000 genomes]
rs11164665	0.80[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11164668	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11164669	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11164672	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11809524	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11811018	1.00[JPT][hapmap]
rs12025848	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12036215	0.80[ASN][1000 genomes]
rs12047268	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12092111	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12118365	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12119459	1.00[JPT][hapmap]
rs12123031	1.00[JPT][hapmap]
rs12124588	1.00[JPT][hapmap]
rs12127590	1.00[JPT][hapmap]
rs12136338	1.00[JPT][hapmap]
rs12136748	1.00[JPT][hapmap]
rs12139120	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12142575	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12723167	1.00[JPT][hapmap]
rs12723922	1.00[JPT][hapmap]
rs12724152	1.00[JPT][hapmap]
rs12726958	1.00[JPT][hapmap]
rs12727959	1.00[JPT][hapmap]
rs12728397	1.00[JPT][hapmap]
rs12729449	1.00[JPT][hapmap]
rs12729602	1.00[JPT][hapmap]
rs12731843	1.00[JPT][hapmap]
rs12733933	1.00[JPT][hapmap]
rs12738133	1.00[JPT][hapmap]
rs12740738	0.94[ASN][1000 genomes]
rs12743365	1.00[JPT][hapmap]
rs12744290	1.00[JPT][hapmap]
rs12744488	1.00[JPT][hapmap]
rs12750377	1.00[JPT][hapmap]
rs12756627	1.00[JPT][hapmap]
rs1337174	1.00[JPT][hapmap]
rs1337175	1.00[JPT][hapmap]
rs1337186	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1337191	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1337195	0.83[MEX][hapmap]
rs1415359	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1415361	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1415364	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1463034	1.00[JPT][hapmap]
rs1463035	1.00[JPT][hapmap]
rs1538041	1.00[JPT][hapmap]
rs1564143	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1591636	1.00[JPT][hapmap]
rs1591637	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17506286	1.00[JPT][hapmap]
rs17507967	1.00[JPT][hapmap]
rs1870958	1.00[JPT][hapmap]
rs1903787	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2050601	1.00[JPT][hapmap]
rs2061704	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2065922	0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2252146	1.00[JPT][hapmap]
rs2254082	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2376280	0.80[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2376281	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2615977	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2615987	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2622848	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2622870	1.00[JPT][hapmap]
rs2622874	1.00[JPT][hapmap]
rs2622876	1.00[JPT][hapmap]
rs2622877	1.00[JPT][hapmap]
rs2622880	1.00[JPT][hapmap]
rs2786120	1.00[JPT][hapmap]
rs2786121	1.00[JPT][hapmap]
rs2786122	1.00[JPT][hapmap]
rs2786125	1.00[JPT][hapmap]
rs2889351	0.94[ASN][1000 genomes]
rs2929163	1.00[JPT][hapmap]
rs3102053	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3767272	0.82[JPT][hapmap]
rs3850459	1.00[JPT][hapmap]
rs3908854	0.80[ASN][1000 genomes]
rs4391683	0.96[ASN][1000 genomes]
rs4478834	1.00[JPT][hapmap]
rs4907986	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4908280	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4908286	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4908289	0.87[ASN][1000 genomes]
rs4908291	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6663034	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6670486	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6672647	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6695665	1.00[JPT][hapmap]
rs7416903	0.83[EUR][1000 genomes]
rs7517682	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7532572	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7544130	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7550118	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs945748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9970114	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522922	chr1:103305021-103764640	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv830893	chr1:103458498-103635579	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv931600	chr1:103548397-104161031	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4338381	DBT	cis	cerebellum	SCAN
rs4338381	AGL	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:103567400-103575000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:103570400-103573400	Active TSS	Brain Germinal Matrix	brain
3	chr1:103570400-103575200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:103571400-103573600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:103571400-103574600	Active TSS	Cortex derived primary cultured neurospheres	brain
6	chr1:103571400-103574800	Active TSS	Fetal Brain Female	brain
7	chr1:103571600-103573000	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr1:103571600-103573200	Active TSS	NH-A	brain
9	chr1:103571600-103574600	Active TSS	HSMMtube	muscle
10	chr1:103571800-103573000	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr1:103571800-103573000	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr1:103571800-103573000	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr1:103571800-103573200	Active TSS	H1 Cell Line	embryonic stem cell
14	chr1:103571800-103574600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:103571800-103574600	Active TSS	Brain Hippocampus Middle	brain
16	chr1:103571800-103574800	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr1:103571800-103574800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:103571800-103574800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:103571800-103575000	Active TSS	Brain Anterior Caudate	brain
20	chr1:103571800-103575000	Active TSS	HSMM	muscle
21	chr1:103571800-103575200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:103571800-103575200	Active TSS	Brain Angular Gyrus	brain
23	chr1:103571800-103575200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:103571800-103575600	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr1:103572000-103573200	Active TSS	Colon Smooth Muscle	Colon
26	chr1:103572000-103573200	Active TSS	Fetal Brain Male	brain
27	chr1:103572000-103573200	Active TSS	Fetal Kidney	kidney
28	chr1:103572000-103573200	Active TSS	Stomach Smooth Muscle	stomach
29	chr1:103572000-103573400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:103572000-103573600	Active TSS	Brain Cingulate Gyrus	brain
31	chr1:103572000-103574000	Active TSS	NHLF	lung
32	chr1:103572000-103574400	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr1:103572000-103574600	Active TSS	Aorta	Aorta
34	chr1:103572000-103574600	Active TSS	Brain Substantia Nigra	brain
35	chr1:103572000-103574600	Active TSS	Right Atrium	heart
36	chr1:103572000-103574600	Active TSS	NHDF-Ad	bronchial
37	chr1:103572000-103574800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr1:103572000-103574800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:103572000-103574800	Active TSS	Fetal Heart	heart
40	chr1:103572000-103575000	Active TSS	H9 Cell Line	embryonic stem cell
41	chr1:103572000-103575200	Active TSS	A549	lung
42	chr1:103572200-103573000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:103572200-103573000	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr1:103572200-103573000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:103572200-103573000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
46	chr1:103572200-103573000	Active TSS	Psoas Muscle	Psoas
47	chr1:103572200-103573400	Active TSS	Fetal Stomach	stomach
48	chr1:103572200-103573800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
49	chr1:103572200-103573800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
50	chr1:103572200-103574600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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