Variant report

Variant	rs357531
Chromosome Location	chr9:98162037-98162038
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10993543	0.82[EUR][1000 genomes]
rs16909865	1.00[AFR][1000 genomes]
rs28517704	1.00[AFR][1000 genomes]
rs357526	0.81[EUR][1000 genomes]
rs357527	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs357530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs357535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs357537	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs357541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs357544	0.82[AMR][1000 genomes]
rs357545	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs357555	1.00[AFR][1000 genomes]
rs357556	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs357560	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs357561	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs357562	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs419574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57247461	1.00[AFR][1000 genomes]
rs613040	0.82[AMR][1000 genomes];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	nsv831657	chr9:97959274-98204769	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1045479	chr9:98115290-98172995	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1051731	chr9:98154815-98201115	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs357531	FANCC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98144000-98172400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:98146600-98168400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr9:98150600-98173600	Weak transcription	Fetal Intestine Small	intestine
4	chr9:98160400-98188400	Weak transcription	Pancreas	Pancrea
5	chr9:98161200-98162200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr9:98161400-98162200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:98161400-98162200	Enhancers	Fetal Muscle Leg	muscle
8	chr9:98161600-98162200	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr9:98161600-98162200	Enhancers	H1 Cell Line	embryonic stem cell
10	chr9:98161600-98162200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:98161800-98172200	Weak transcription	ES-WA7 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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