Variant report

Variant	rs10518316
Chromosome Location	chr4:119883564-119883565
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10017229	0.84[JPT][hapmap]
rs10434026	0.81[ASN][1000 genomes]
rs11939869	1.00[YRI][hapmap]
rs13108576	0.81[ASN][1000 genomes]
rs13111284	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13117365	0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13151719	0.90[AFR][1000 genomes]
rs17050208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17050228	0.84[JPT][hapmap]
rs17327171	1.00[LWK][hapmap]
rs28667954	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36116256	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9307465	0.84[MEX][hapmap]

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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	esv992928	chr4:119880696-119889458	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10518316	NDST3	cis	cerebellum	SCAN
rs10518316	PRSS12	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119868800-119886000	Weak transcription	Fetal Stomach	stomach
2	chr4:119874200-119886000	Enhancers	Rectal Smooth Muscle	rectum
3	chr4:119875200-119885800	Weak transcription	NHLF	lung
4	chr4:119876400-119886000	Weak transcription	Aorta	Aorta
5	chr4:119878600-119885400	Weak transcription	Right Ventricle	heart
6	chr4:119879200-119889000	Weak transcription	Fetal Heart	heart
7	chr4:119879400-119884000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr4:119879800-119883800	Weak transcription	Right Atrium	heart
9	chr4:119879800-119886000	Weak transcription	Psoas Muscle	Psoas
10	chr4:119879800-119893400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:119880000-119884000	Weak transcription	Left Ventricle	heart
12	chr4:119882200-119884200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr4:119882400-119883600	Enhancers	Colon Smooth Muscle	Colon
14	chr4:119882600-119885200	Enhancers	Stomach Smooth Muscle	stomach
15	chr4:119882800-119884000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:119883200-119883800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:119883200-119884200	Enhancers	Adipose Nuclei	Adipose
18	chr4:119883200-119884200	Enhancers	Ovary	ovary
19	chr4:119883200-119884200	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr4:119883400-119884200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:119883400-119884200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:119883400-119884400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:119883400-119886200	Weak transcription	Brain Anterior Caudate	brain

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