Variant report

Variant	rs11729426
Chromosome Location	chr4:101034456-101034457
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10029894	0.96[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11732283	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12649983	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4128310	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4235442	0.81[EUR][1000 genomes]
rs4593140	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4635824	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4699389	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs4699391	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4699392	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4699770	0.96[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4699773	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4699774	0.87[CEU][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55705206	0.81[ASN][1000 genomes]
rs61294522	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62306122	0.81[ASN][1000 genomes]
rs62306150	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62307560	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6532843	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6834862	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6837281	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6840267	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6856293	0.96[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs7671507	0.90[ASN][1000 genomes]
rs7671736	0.96[CEU][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7682156	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7697932	0.84[ASN][1000 genomes]
rs7698869	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427689	chr4:100931741-101216531	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv830019	chr4:101023666-101208908	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11729426	DDIT4L	cis	lymphoblastoid	seeQTL
rs11729426	ADH5	cis	cerebellum	SCAN
rs11729426	C4orf37	cis	cerebellum	SCAN
rs11729426	DNAJB14	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:101032000-101035000	Weak transcription	Fetal Intestine Large	intestine
2	chr4:101033200-101035200	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr4:101033800-101035400	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr4:101033800-101035600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr4:101034200-101037400	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr4:101034200-101037800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr4:101034400-101034800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr4:101034400-101034800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:101034400-101035200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:101034400-101035200	Enhancers	Brain Anterior Caudate	brain
11	chr4:101034400-101035400	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr4:101034400-101035600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:101034400-101037000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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