Variant report

Variant	rs9880635
Chromosome Location	chr3:42807127-42807128
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	chr3:42804568..42808047-chr3:42844352..42847705,4	K562	blood:

Variant related genes	Relation type
ENSG00000144648	Chromatin interaction
ENSG00000181061	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10865923	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11129969	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs11129970	0.81[EUR][1000 genomes]
rs11709054	0.81[EUR][1000 genomes]
rs11709500	0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs11710120	0.93[ASN][1000 genomes]
rs11713172	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs11717346	0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11915803	0.85[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17238314	0.81[EUR][1000 genomes]
rs17238798	0.81[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2240861	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs339664	0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs339667	0.99[ASN][1000 genomes]
rs339668	0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs339676	0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs34110933	0.81[EUR][1000 genomes]
rs4682856	0.94[GIH][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs4682857	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4683336	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55884426	0.81[EUR][1000 genomes]
rs55904344	0.82[EUR][1000 genomes]
rs58045017	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59713146	0.81[EUR][1000 genomes]
rs62246603	0.82[EUR][1000 genomes]
rs62246606	0.81[EUR][1000 genomes]
rs62246629	0.93[EUR][1000 genomes]
rs62246635	0.82[EUR][1000 genomes]
rs62246636	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6442057	0.84[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs6764909	0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7634876	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013578	chr3:42747858-42817321	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv999713	chr3:42749022-42817321	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv1846968	chr3:42787469-42832979	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9880635	HHATL	cis	parietal	SCAN
rs9880635	ULK4	cis	cerebellum	SCAN
rs9880635	LRRC2	cis	cerebellum	SCAN
rs9880635	EXOSC7	cis	cerebellum	SCAN
rs9880635	FYCO1	cis	cerebellum	SCAN
rs9880635	HHATL	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42778000-42811000	Weak transcription	Spleen	Spleen
2	chr3:42789800-42807600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:42791800-42807200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:42793600-42811000	Weak transcription	Lung	lung
5	chr3:42795600-42814000	Weak transcription	Gastric	stomach
6	chr3:42795600-42814400	Weak transcription	Aorta	Aorta
7	chr3:42800400-42808600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr3:42803000-42814200	Weak transcription	Right Atrium	heart
9	chr3:42804200-42814200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:42804400-42807400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:42804800-42807400	Weak transcription	Adipose Nuclei	Adipose
12	chr3:42805000-42807400	Weak transcription	HepG2	liver
13	chr3:42805000-42813800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:42805800-42807600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:42805800-42807800	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr3:42805800-42808400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr3:42806000-42807400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:42806200-42807200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:42806200-42809800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:42806400-42807200	Weak transcription	Primary B cells from cord blood	blood
21	chr3:42806800-42807600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:42807000-42807600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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