Variant report

Variant	rs7459881
Chromosome Location	chr8:64276115-64276116
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10103710	0.87[ASN][1000 genomes]
rs10156375	0.89[ASN][1000 genomes]
rs1030584	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1030585	0.87[ASN][1000 genomes]
rs1030586	0.87[ASN][1000 genomes]
rs10957282	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10957283	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11777208	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11779425	0.81[JPT][hapmap];0.84[YRI][hapmap]
rs11783042	0.81[JPT][hapmap];0.84[YRI][hapmap]
rs11783055	0.81[JPT][hapmap]
rs11786252	0.81[JPT][hapmap];0.84[YRI][hapmap]
rs12544518	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12545091	0.82[ASW][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap]
rs13265562	0.81[JPT][hapmap]
rs13277482	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs16930415	0.87[ASN][1000 genomes]
rs28540225	0.87[ASN][1000 genomes]
rs28696311	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35674021	0.86[ASN][1000 genomes]
rs4739089	0.82[ASW][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap]
rs56033239	0.93[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6472093	0.98[ASN][1000 genomes]
rs6472094	0.96[ASN][1000 genomes]
rs6472095	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6472096	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6472097	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6472103	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6472104	0.84[ASN][1000 genomes]
rs6980685	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6981013	0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6981563	0.89[ASN][1000 genomes]
rs6993493	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6994236	0.81[JPT][hapmap]
rs7016013	0.93[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7459926	0.93[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7460026	0.93[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7464324	0.93[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7818456	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7840470	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7841852	0.82[ASW][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap]
rs7841909	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9298075	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9298077	0.82[ASW][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap]

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	nsv831342	chr8:64084331-64294941	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv890967	chr8:64107847-64454446	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7459881	CHD7	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:64274800-64277000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr8:64274800-64278000	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr8:64274800-64278400	Enhancers	H1 Cell Line	embryonic stem cell
4	chr8:64274800-64278600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr8:64274800-64279200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr8:64274800-64279200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr8:64275000-64276400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr8:64275000-64276600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr8:64275000-64276800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr8:64275000-64278200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr8:64275200-64278200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr8:64275400-64276200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr8:64275400-64276200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr8:64275400-64276200	Enhancers	Fetal Muscle Leg	muscle
15	chr8:64275400-64277000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr8:64275600-64276600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr8:64275600-64276800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr8:64275600-64276800	Enhancers	Brain Germinal Matrix	brain
19	chr8:64275800-64276200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr8:64275800-64276600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr8:64275800-64276800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr8:64275800-64277000	Enhancers	Brain Substantia Nigra	brain
23	chr8:64275800-64278000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr8:64275800-64279000	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr8:64276000-64276400	Weak transcription	Brain Hippocampus Middle	brain
26	chr8:64276000-64277000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr8:64276000-64278400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr8:64276000-64278800	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr8:64276000-64279200	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr8:64276000-64279400	Enhancers	HUES64 Cell Line	embryonic stem cell

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