Variant report

Variant	rs12440563
Chromosome Location	chr15:74060297-74060298
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1038093	0.81[JPT][hapmap]
rs12442096	0.82[AFR][1000 genomes]
rs17187183	0.96[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs2123208	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28485305	0.81[AMR][1000 genomes]
rs28594180	0.81[AFR][1000 genomes]
rs28688071	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3743098	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4243087	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4887161	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4887164	0.95[ASN][1000 genomes]
rs60833441	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7162423	0.93[ASW][hapmap];0.96[CEU][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7171779	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7172656	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471252	chr15:74006691-74089793	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12440563	COMMD4	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74053000-74067000	Weak transcription	Fetal Brain Male	brain
2	chr15:74057200-74060400	Weak transcription	Esophagus	oesophagus
3	chr15:74057200-74066000	Weak transcription	Right Atrium	heart
4	chr15:74057400-74066400	Weak transcription	Right Ventricle	heart
5	chr15:74058800-74061000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:74059000-74061200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:74059400-74062200	Weak transcription	Gastric	stomach
8	chr15:74059600-74060800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr15:74059600-74060800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:74059800-74060400	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr15:74059800-74060400	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr15:74059800-74060400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:74059800-74060600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr15:74059800-74060800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:74059800-74060800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr15:74059800-74060800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr15:74059800-74061800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr15:74060000-74060400	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr15:74060000-74060600	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr15:74060000-74060600	Enhancers	H9 Cell Line	embryonic stem cell
21	chr15:74060000-74060800	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr15:74060000-74060800	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr15:74060000-74060800	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr15:74060200-74060400	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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