Variant report

Variant	rs6762678
Chromosome Location	chr3:21698690-21698691
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12633967	0.84[GIH][hapmap]
rs12636280	0.90[ASN][1000 genomes]
rs12638523	0.86[CEU][hapmap]
rs13081227	0.81[CEU][hapmap]
rs1320290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1320291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17009183	0.95[JPT][hapmap]
rs17009199	0.85[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs3821396	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60445541	0.86[ASN][1000 genomes]
rs62237406	0.85[ASN][1000 genomes]
rs62237408	0.87[ASN][1000 genomes]
rs62237409	0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs62237411	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62237412	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62237415	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62237416	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62237417	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62237418	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62237419	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6764199	0.80[CEU][hapmap]
rs6775498	0.80[CEU][hapmap];0.93[MEX][hapmap]
rs9310655	0.81[CEU][hapmap]
rs9810547	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9859099	0.86[CEU][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap]
rs9862240	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534005	chr3:21387588-22003293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1010460	chr3:21516810-21839871	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834631	chr3:21612283-21763887	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv1007048	chr3:21666807-21865229	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv536516	chr3:21666807-21865229	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv589896	chr3:21692393-21712269	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6762678	NKIRAS1	cis	cerebellum	SCAN
rs6762678	RAB5A	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:21683800-21706600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:21685600-21707200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:21687200-21701800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:21687200-21706200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:21687200-21709600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:21687400-21706800	Weak transcription	Fetal Lung	lung
7	chr3:21688000-21699000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:21688000-21707000	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:21695000-21703600	Weak transcription	K562	blood
10	chr3:21696600-21698800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:21696600-21713400	Weak transcription	Fetal Heart	heart
12	chr3:21696800-21713200	Weak transcription	NHDF-Ad	bronchial
13	chr3:21697000-21704400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:21697200-21706200	Weak transcription	Aorta	Aorta

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