Variant report

Variant	rs2244306
Chromosome Location	chr4:147289062-147289063
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10012310	0.86[MEX][hapmap]
rs10017463	0.80[MEX][hapmap]
rs10023228	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11726594	0.86[MEX][hapmap]
rs13105153	0.86[MEX][hapmap]
rs13110748	0.86[MEX][hapmap]
rs13114641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13121951	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1352066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1352068	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1485950	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2356822	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2630276	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2630279	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2630283	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630287	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2679122	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2679129	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2679133	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2679137	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2679138	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2679139	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2679152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4092340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4103540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4407528	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4516736	1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes]
rs4835032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4835300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835310	0.86[MEX][hapmap]
rs6537412	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6537413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6537421	0.86[MEX][hapmap]
rs6852118	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857518	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7670877	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7682719	1.00[JPT][hapmap];0.80[MEX][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap]
rs7686137	0.90[JPT][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap]
rs7691153	0.84[CEU][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs923164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs923165	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9308200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9784489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461675	chr4:147116864-147768206	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv595651	chr4:147116864-147768206	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1033640	chr4:147232217-147531881	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv917053	chr4:147265436-147499653	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1023868	chr4:147265443-147531626	Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv537293	chr4:147265443-147531626	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
7	esv3400231	chr4:147269396-147292066	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2244306	OTUD4	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147276200-147292400	Weak transcription	Aorta	Aorta
2	chr4:147277400-147314200	Weak transcription	Left Ventricle	heart
3	chr4:147283000-147332200	Weak transcription	Primary B cells from cord blood	blood
4	chr4:147287200-147293400	Weak transcription	Pancreas	Pancrea
5	chr4:147287600-147292000	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr4:147288000-147289200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:147288000-147290400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:147288000-147290400	Enhancers	Brain Angular Gyrus	brain
9	chr4:147288000-147292400	Enhancers	Fetal Heart	heart
10	chr4:147288200-147289800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:147288200-147289800	Enhancers	Brain Cingulate Gyrus	brain
12	chr4:147288200-147290400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:147288400-147289600	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr4:147288400-147290000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:147288800-147289400	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr4:147288800-147289400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:147288800-147289400	Enhancers	Fetal Brain Female	brain
18	chr4:147288800-147289400	Enhancers	Rectal Smooth Muscle	rectum
19	chr4:147288800-147289600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:147288800-147293800	Enhancers	HUVEC	blood vessel
21	chr4:147289000-147289200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:147289000-147289400	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr4:147289000-147289400	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr4:147289000-147289400	Flanking Active TSS	Brain Substantia Nigra	brain
25	chr4:147289000-147289600	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr4:147289000-147289600	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr4:147289000-147289600	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr4:147289000-147289800	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr4:147289000-147289800	Enhancers	Brain Hippocampus Middle	brain
30	chr4:147289000-147289800	Enhancers	Colon Smooth Muscle	Colon
31	chr4:147289000-147290200	Enhancers	Primary hematopoietic stem cells	blood
32	chr4:147289000-147291800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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