Variant report

Variant	rs17422275
Chromosome Location	chr6:118611041-118611042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10499086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1319987	0.82[CHB][hapmap]
rs1319988	0.82[CHB][hapmap]
rs1321985	0.94[ASN][1000 genomes]
rs1630266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1690658	0.94[ASN][1000 genomes]
rs1690664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1690667	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17079881	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1743256	0.88[ASN][1000 genomes]
rs1743257	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1743258	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1743259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1761620	0.94[ASN][1000 genomes]
rs1761622	0.94[ASN][1000 genomes]
rs1761624	0.88[ASN][1000 genomes]
rs1889468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs25422	0.82[CHB][hapmap]
rs3734345	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3851206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3900941	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3901856	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3904613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62421485	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62421486	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62421489	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62421532	1.00[AFR][1000 genomes]
rs6924560	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724868	0.82[CHB][hapmap]
rs7453860	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9372498	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937275	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9489407	0.82[CHB][hapmap]
rs9489409	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530526	chr6:118027339-118718476	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv532051	chr6:118551027-119044197	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1020463	chr6:118593028-119146363	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17422275	FAM26D	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118606600-118613400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr6:118607600-118614000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:118607600-118616000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:118607600-118617000	Weak transcription	Fetal Muscle Leg	muscle
5	chr6:118608200-118613400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr6:118608400-118613400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr6:118608400-118613400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr6:118608600-118612800	Weak transcription	Colon Smooth Muscle	Colon
9	chr6:118609000-118616400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:118609400-118612600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr6:118609800-118616600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:118610000-118614800	Weak transcription	Aorta	Aorta
13	chr6:118610200-118617200	Weak transcription	Left Ventricle	heart
14	chr6:118610400-118611200	Enhancers	Fetal Heart	heart

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