Variant report

Variant	rs35874
Chromosome Location	chr3:118700783-118700784
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1521296	0.95[EUR][1000 genomes]
rs1521299	0.87[AMR][1000 genomes]
rs251456	0.84[CHB][hapmap];0.80[JPT][hapmap];0.87[EUR][1000 genomes]
rs2573192	0.98[ASN][1000 genomes]
rs35872	1.00[ASW][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71325350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs859021	0.84[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv1010475	chr3:118657382-118789714	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv877369	chr3:118681771-118824418	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv2756586	chr3:118688611-118863998	Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35874	FBXO40	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118688800-118706000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:118689000-118703600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:118692600-118704400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:118693400-118704400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:118697200-118703600	Weak transcription	Ovary	ovary
6	chr3:118697400-118702800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:118697400-118704200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:118697400-118704800	Weak transcription	Pancreas	Pancrea
9	chr3:118697600-118704200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:118699200-118706000	Enhancers	Brain Substantia Nigra	brain
11	chr3:118700000-118701000	Weak transcription	Brain Anterior Caudate	brain
12	chr3:118700000-118701200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:118700000-118704600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:118700200-118706200	Enhancers	Brain Hippocampus Middle	brain
15	chr3:118700400-118701000	Enhancers	Psoas Muscle	Psoas
16	chr3:118700400-118705800	Enhancers	Brain Cingulate Gyrus	brain
17	chr3:118700400-118706000	Enhancers	Brain Angular Gyrus	brain
18	chr3:118700400-118707800	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr3:118700600-118700800	Enhancers	Right Atrium	heart
20	chr3:118700600-118700800	Enhancers	K562	blood

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