Variant report

Variant	rs130559
Chromosome Location	chr22:33188536-33188537
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	22:32920308-32927723..22:33186569-33190123	H1-hESC	embryonic stem cell:	embryo
2	chr22:33054648..33057436-chr22:33186906..33189165,2	MCF-7	breast:
3	chr22:33187359..33190243-chr22:33196094..33197933,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185666	Chromatin interaction
ENSG00000100234	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1018792	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11089594	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs130269	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs130270	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs130274	0.90[CHB][hapmap];0.92[GIH][hapmap]
rs130275	1.00[ASW][hapmap];0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs130276	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs130287	1.00[ASW][hapmap];0.87[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.92[GIH][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs130525	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs130530	0.92[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs130532	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs130533	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs130538	1.00[CEU][hapmap];0.80[CHB][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs130548	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs130551	0.83[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs130560	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs135149	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1962223	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2413148	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4635627	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4821094	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4821095	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4821096	0.94[CEU][hapmap];0.90[CHB][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs5754251	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs5994619	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs5998616	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs5998622	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72487604	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs762887	0.94[CEU][hapmap];0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs80269	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs929013	0.94[CEU][hapmap];0.90[CHB][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs929014	0.94[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9606991	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9606992	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9606993	0.94[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9609622	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9609623	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9609631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	nsv1061384	chr22:33165464-33191811	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs130559	INPP5J	cis	cerebellum	SCAN
rs130559	KREMEN1	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33176800-33191200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr22:33176800-33196600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr22:33177400-33192800	Weak transcription	Pancreas	Pancrea
4	chr22:33182000-33192800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr22:33182600-33195400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr22:33185200-33190200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr22:33185200-33190600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr22:33185200-33192600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr22:33185200-33192600	Weak transcription	Right Atrium	heart
10	chr22:33185200-33192800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr22:33185200-33197200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr22:33185400-33191400	Weak transcription	Right Ventricle	heart
13	chr22:33185600-33189200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr22:33185600-33189800	Weak transcription	Fetal Muscle Leg	muscle
15	chr22:33185600-33189800	Weak transcription	Fetal Stomach	stomach
16	chr22:33185800-33190600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr22:33185800-33192400	Weak transcription	NHDF-Ad	bronchial
18	chr22:33186000-33190000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr22:33186000-33190600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr22:33186000-33190600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr22:33186000-33190800	Weak transcription	Placenta	Placenta
22	chr22:33186000-33191400	Weak transcription	Adipose Nuclei	Adipose
23	chr22:33186000-33192400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr22:33186000-33192400	Weak transcription	HSMMtube	muscle
25	chr22:33186000-33192600	Weak transcription	HSMM	muscle
26	chr22:33186200-33190600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr22:33186200-33190800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr22:33187600-33188800	Weak transcription	HepG2	liver
29	chr22:33187600-33192800	Weak transcription	Rectal Mucosa Donor 31	rectum

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