Variant report

Variant	rs1879202
Chromosome Location	chr8:89297906-89297907
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10100297	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955556	0.84[AMR][1000 genomes]
rs11986810	0.81[AMR][1000 genomes]
rs13277770	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1394514	0.91[CEU][hapmap]
rs1401864	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1504804	0.91[CEU][hapmap]
rs1519930	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1915018	0.80[AMR][1000 genomes]
rs1915024	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3844198	0.84[AMR][1000 genomes]
rs4147332	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4246112	0.91[CEU][hapmap]
rs4246113	0.91[CEU][hapmap]
rs4463475	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4515601	0.91[CEU][hapmap]
rs4961087	0.91[CEU][hapmap]
rs7842943	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029898	chr8:88837956-89606641	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1030028	chr8:89060085-89733470	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1019111	chr8:89186908-89475460	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv831386	chr8:89209788-89403546	Enhancers Genic enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv891170	chr8:89227970-89298199	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1879202	MMP16	cis	Thyroid	GTEx
rs1879202	NBN	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:89282400-89299200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr8:89288800-89301400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr8:89289200-89299200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr8:89289800-89299400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr8:89289800-89299400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr8:89290200-89300600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr8:89290800-89299600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr8:89293800-89309800	Weak transcription	Aorta	Aorta
9	chr8:89294200-89309400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr8:89294200-89309400	Weak transcription	NHDF-Ad	bronchial
11	chr8:89296400-89300800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr8:89296600-89299800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr8:89297000-89299400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr8:89297200-89298200	Weak transcription	Fetal Heart	heart
15	chr8:89297200-89299200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr8:89297200-89299400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr8:89297200-89299600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr8:89297200-89300000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr8:89297400-89299400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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