Variant report

Variant	rs13139234
Chromosome Location	chr4:77029613-77029614
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:77027487..77029799-chr4:77068169..77070683,2	K562	blood:
2	chr4:76961032..76963158-chr4:77027696..77030643,2	K562	blood:

Variant related genes	Relation type
ENSG00000169248	Chromatin interaction
ENSG00000138750	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10017484	1.00[CHB][hapmap]
rs10022137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10022519	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10030683	1.00[ASN][1000 genomes]
rs11097232	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12331521	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4241591	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs4274876	1.00[ASN][1000 genomes]
rs4440243	0.92[ASN][1000 genomes]
rs4524416	0.83[AFR][1000 genomes]
rs4544733	0.90[YRI][hapmap]
rs4624679	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.84[ASN][1000 genomes]
rs4859613	1.00[ASN][1000 genomes]
rs4859619	0.84[ASN][1000 genomes]
rs6532181	1.00[ASN][1000 genomes]
rs6532208	0.88[YRI][hapmap]
rs6814012	1.00[CHB][hapmap]
rs6814817	1.00[CHB][hapmap]
rs6856609	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72655511	0.90[AFR][1000 genomes]
rs72655512	0.90[AFR][1000 genomes]
rs72655515	0.91[AFR][1000 genomes]
rs7654988	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7657598	0.85[YRI][hapmap]
rs7682766	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7697711	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.92[ASN][1000 genomes]
rs9990550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9992976	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[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	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats 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 target site	38 gene(s)	inside rSNPs	diseases
2	nsv1009047	chr4:76989180-77077885	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13139234	NUP54	cis	parietal	SCAN
rs13139234	ART3	cis	Nerve Tibial	GTEx
rs13139234	NUP54	cis	cerebellum	SCAN
rs13139234	ANTXR2	cis	cerebellum	SCAN
rs13139234	CCDC158	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77017000-77034400	Weak transcription	Right Ventricle	heart
2	chr4:77024000-77032200	Weak transcription	Left Ventricle	heart
3	chr4:77026400-77033400	Weak transcription	HSMMtube	muscle
4	chr4:77026600-77033400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr4:77027200-77033000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr4:77027200-77033400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:77027200-77034000	Weak transcription	Brain Anterior Caudate	brain
8	chr4:77027200-77034400	Weak transcription	Fetal Muscle Leg	muscle
9	chr4:77027200-77035400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr4:77027600-77033400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:77027600-77034200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr4:77027600-77034400	Weak transcription	Brain Hippocampus Middle	brain
13	chr4:77027600-77037400	Weak transcription	Brain Substantia Nigra	brain
14	chr4:77027800-77034200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr4:77027800-77034200	Weak transcription	Fetal Brain Female	brain
16	chr4:77027800-77036400	Weak transcription	Brain Angular Gyrus	brain
17	chr4:77027800-77038400	Weak transcription	Fetal Brain Male	brain
18	chr4:77028000-77033200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:77028000-77034000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:77028000-77037600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr4:77028000-77068600	Weak transcription	Gastric	stomach
22	chr4:77028400-77033200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:77028400-77033400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr4:77028400-77034400	Weak transcription	K562	blood
25	chr4:77029200-77033800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr4:77029600-77030000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:77029600-77033400	Weak transcription	HSMM	muscle

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