Variant report

Variant	rs213977
Chromosome Location	chr7:117238445-117238446
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs117243	1.00[YRI][hapmap]
rs1208525	0.82[CEU][hapmap];0.94[CHB][hapmap]
rs1208528	0.82[CEU][hapmap];0.94[CHB][hapmap]
rs12534186	1.00[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs177284	0.82[ASN][1000 genomes]
rs2106155	0.94[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs213934	0.83[ASW][hapmap];0.84[GIH][hapmap];0.87[YRI][hapmap]
rs213935	0.80[GIH][hapmap]
rs213950	0.82[GIH][hapmap]
rs213953	1.00[YRI][hapmap]
rs213963	1.00[YRI][hapmap]
rs213964	1.00[YRI][hapmap]
rs213965	0.92[ASW][hapmap];0.86[GIH][hapmap];1.00[YRI][hapmap]
rs213966	1.00[YRI][hapmap]
rs213967	1.00[YRI][hapmap]
rs213968	1.00[YRI][hapmap]
rs213971	0.91[ASW][hapmap];0.89[GIH][hapmap];1.00[YRI][hapmap]
rs213976	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs213983	0.88[ASN][1000 genomes]
rs213985	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs213987	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs214152	0.89[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap]
rs214160	0.80[ASN][1000 genomes]
rs214167	1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.89[ASN][1000 genomes]
rs2237726	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs2246450	0.94[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs2254742	1.00[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs2283058	1.00[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2299445	1.00[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs2402229	0.82[CEU][hapmap];0.94[CHB][hapmap]
rs35278595	0.84[ASN][1000 genomes]
rs3735645	0.92[ASW][hapmap];0.85[CEU][hapmap];0.85[CHD][hapmap];0.92[MEX][hapmap]
rs4148714	0.93[ASN][1000 genomes]
rs4148724	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs43025	0.80[GIH][hapmap]
rs43033	0.80[GIH][hapmap]
rs6466619	0.82[CEU][hapmap];0.87[YRI][hapmap]
rs6978581	0.92[ASW][hapmap];0.82[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.92[MEX][hapmap]
rs756665	0.80[GIH][hapmap]
rs7793030	0.89[CHB][hapmap]
rs7797932	1.00[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs7810506	0.82[GIH][hapmap]
rs885993	0.80[GIH][hapmap]
rs975722	0.92[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889078	chr7:117135025-117246315	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv889082	chr7:117203417-117246315	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv889083	chr7:117203417-117256374	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv889084	chr7:117212723-117246315	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv889085	chr7:117214089-117246315	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv889086	chr7:117214089-117252873	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv889087	chr7:117226766-117246315	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv608257	chr7:117229167-117241394	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs213977	PPP1R3A	cis	parietal	SCAN
rs213977	ING3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117233000-117245000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr7:117234600-117240400	Weak transcription	A549	lung
3	chr7:117236200-117243400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr7:117236200-117244800	Weak transcription	Pancreas	Pancrea
5	chr7:117236200-117245600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:117236600-117245600	Weak transcription	Colonic Mucosa	Colon
7	chr7:117236800-117244800	Weak transcription	Fetal Intestine Large	intestine
8	chr7:117237600-117245000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr7:117238200-117242000	Weak transcription	Fetal Intestine Small	intestine
10	chr7:117238200-117243600	Weak transcription	Fetal Thymus	thymus
11	chr7:117238200-117243600	Weak transcription	Dnd41	blood

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