Variant report

Variant	rs7976
Chromosome Location	chr19:35978299-35978300
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10410228	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10414731	1.00[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes]
rs10417830	1.00[CHD][hapmap]
rs10421540	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11880364	1.00[CEU][hapmap];0.82[MEX][hapmap];0.94[EUR][1000 genomes]
rs11880530	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17638216	1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17705401	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17705416	1.00[ASN][1000 genomes]
rs17705450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28561458	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59551721	0.91[EUR][1000 genomes]
rs62111717	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6510489	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7253910	0.80[CEU][hapmap];0.97[EUR][1000 genomes]
rs8106676	0.90[EUR][1000 genomes]
rs8107732	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9973222	1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv833811	chr19:35850257-36029535	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1057692	chr19:35949892-35984103	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	nsv543994	chr19:35949892-35984103	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7976	ZNF428	cis	parietal	SCAN
rs7976	PSG1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35976400-35978400	Enhancers	Fetal Intestine Small	intestine
2	chr19:35976600-35978400	Enhancers	Fetal Intestine Large	intestine
3	chr19:35977200-35978600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:35977400-35978600	Weak transcription	Fetal Lung	lung
5	chr19:35977600-35978800	Enhancers	HepG2	liver
6	chr19:35978200-35978600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:35978200-35978600	Weak transcription	Pancreas	Pancrea

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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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