Variant report

Variant	rs9816126
Chromosome Location	chr3:155865255-155865256
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	chr3:155864395..155866159-chr3:155866850..155868427,2	K562	blood:
2	chr3:155848600..155850678-chr3:155862966..155865880,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10936024	1.00[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs11709514	0.94[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs11716256	0.85[ASN][1000 genomes]
rs11718399	0.94[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs13073556	0.94[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs13093154	0.89[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs1488425	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs4234308	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4261831	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs4359773	0.97[ASN][1000 genomes]
rs4359774	0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs4605502	1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[ASN][1000 genomes]
rs4679760	0.86[ASN][1000 genomes]
rs4679761	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs4680232	0.94[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs4680233	0.94[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs4680234	0.86[ASN][1000 genomes]
rs4680235	0.89[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs4680237	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs4680238	0.89[MEX][hapmap]
rs56231269	0.91[ASN][1000 genomes]
rs62284939	0.91[ASN][1000 genomes]
rs6441034	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441035	1.00[CHB][hapmap];0.87[JPT][hapmap];0.97[ASN][1000 genomes]
rs6441036	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441045	0.83[MEX][hapmap]
rs6761966	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6778035	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs6780500	0.92[ASN][1000 genomes]
rs6788449	0.94[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6793964	0.94[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs7617796	0.94[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs7618820	0.94[CHB][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs7629439	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7633081	0.90[ASN][1000 genomes]
rs9289961	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs9289962	0.83[MEX][hapmap]
rs9814661	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs9838322	0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs9842620	0.94[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs9856468	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs9861320	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs9862153	0.94[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs9869649	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9870793	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9882088	1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[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	nsv592085	chr3:155827634-156012679	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9816126	SCARNA7	cis	cerebellum	SCAN
rs9816126	MLF1	cis	parietal	SCAN
rs9816126	VEPH1	cis	cerebellum	SCAN
rs9816126	OTOL1	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155861200-155865600	Weak transcription	Pancreas	Pancrea
2	chr3:155861200-155866600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:155861200-155866800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:155862200-155868400	Enhancers	Fetal Brain Male	brain
5	chr3:155862400-155866000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:155862400-155866800	Weak transcription	Right Atrium	heart
7	chr3:155863000-155869800	Weak transcription	Left Ventricle	heart
8	chr3:155863600-155868800	Weak transcription	Ovary	ovary
9	chr3:155864000-155866800	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:155864000-155866800	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:155864200-155867000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:155864400-155866800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:155864600-155865600	Weak transcription	Aorta	Aorta
14	chr3:155864600-155866600	Weak transcription	Fetal Stomach	stomach
15	chr3:155864600-155866800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:155864800-155866000	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:155864800-155866800	Weak transcription	Brain Substantia Nigra	brain
18	chr3:155865000-155866600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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