Variant report

Variant	rs7827941
Chromosome Location	chr8:102841031-102841032
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:97272466..97274308-chr8:102840170..102842402,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156471	Chromatin interaction
ENSG00000156469	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1073373	0.83[CEU][hapmap]
rs1074703	0.82[EUR][1000 genomes]
rs10808378	0.82[CEU][hapmap]
rs10808379	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10955274	0.82[CEU][hapmap]
rs1111886	0.82[CEU][hapmap];0.80[TSI][hapmap]
rs1144545	0.87[CEU][hapmap]
rs1148497	0.87[CEU][hapmap]
rs1148499	0.87[CEU][hapmap]
rs11782123	0.82[CEU][hapmap]
rs12334693	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs1264930	1.00[CEU][hapmap]
rs1264931	0.88[CEU][hapmap]
rs1264933	0.88[CEU][hapmap]
rs12677525	0.83[CEU][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs13251735	0.88[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13255004	0.92[EUR][1000 genomes]
rs1465167	0.84[CHD][hapmap]
rs1557336	0.83[CEU][hapmap]
rs17406994	0.82[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs1893366	0.88[CEU][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs2155938	1.00[CEU][hapmap]
rs2155939	0.88[CEU][hapmap]
rs2155940	0.92[CEU][hapmap]
rs2155941	0.92[CEU][hapmap]
rs2155942	0.96[CEU][hapmap];0.95[CHB][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2155943	0.95[EUR][1000 genomes]
rs2226724	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2226725	0.91[EUR][1000 genomes]
rs28837777	0.81[EUR][1000 genomes]
rs2892324	0.85[CEU][hapmap]
rs4576401	0.81[EUR][1000 genomes]
rs472638	0.87[CEU][hapmap]
rs472963	0.87[CEU][hapmap]
rs4734595	0.83[CEU][hapmap];0.90[TSI][hapmap]
rs4734596	0.82[EUR][1000 genomes]
rs4734597	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs478917	0.87[CEU][hapmap]
rs479041	0.87[CEU][hapmap]
rs480570	0.87[CEU][hapmap]
rs481545	0.87[CEU][hapmap]
rs482023	0.83[CEU][hapmap]
rs486196	0.82[CEU][hapmap]
rs487863	0.83[CEU][hapmap]
rs488034	0.87[CEU][hapmap]
rs489973	0.87[CEU][hapmap]
rs494352	0.82[CEU][hapmap]
rs495636	0.87[CEU][hapmap]
rs513472	0.87[CEU][hapmap]
rs517868	0.83[CEU][hapmap]
rs519197	0.87[CEU][hapmap]
rs520880	0.87[CEU][hapmap]
rs529684	0.87[CEU][hapmap]
rs531624	0.87[CEU][hapmap]
rs540459	0.87[CEU][hapmap]
rs549281	0.87[CEU][hapmap]
rs550281	0.83[CEU][hapmap]
rs551295	0.83[CEU][hapmap]
rs562037	0.86[CEU][hapmap]
rs563463	0.87[CEU][hapmap]
rs566315	0.87[CEU][hapmap]
rs566392	0.87[CEU][hapmap]
rs568194	0.87[CEU][hapmap]
rs569015	0.87[CEU][hapmap]
rs569787	0.85[CEU][hapmap]
rs577756	0.87[CEU][hapmap]
rs6468793	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs6468794	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs6468795	0.82[CEU][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs6468796	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs6468798	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs6468799	0.83[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs6468801	1.00[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6984260	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs6988793	0.81[CHD][hapmap]
rs6991592	0.88[CEU][hapmap]
rs6993577	0.92[EUR][1000 genomes]
rs7000357	0.84[CEU][hapmap];0.95[CHB][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7008826	0.80[TSI][hapmap]
rs7009385	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs7011941	0.84[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7012512	0.86[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs7015311	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs7017754	0.82[CEU][hapmap]
rs7813132	0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7827304	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7827691	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7828175	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs7828516	0.88[CEU][hapmap]
rs7829693	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs7830291	0.84[CHD][hapmap]
rs7835223	0.84[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7835485	0.83[CEU][hapmap]
rs7838696	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7840760	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs8181022	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs8181025	0.84[CEU][hapmap];0.95[CHB][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9297313	0.88[CEU][hapmap]
rs9693504	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018653	chr8:102818271-103009082	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv539700	chr8:102818271-103009082	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv518162	chr8:102841031-102893626	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv523850	chr8:102841031-102893626	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7827941	FOXL1	trans	parietal	SCAN
rs7827941	NCALD	cis	parietal	SCAN
rs7827941	C8orf56	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:102803600-102870600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr8:102832200-102843800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr8:102834800-102843800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:102835000-102844400	Weak transcription	Psoas Muscle	Psoas
5	chr8:102835000-102852000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr8:102836200-102844400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr8:102836600-102844000	Weak transcription	Fetal Heart	heart
8	chr8:102836600-102844200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr8:102836800-102843800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr8:102837200-102844000	Weak transcription	Brain Angular Gyrus	brain
11	chr8:102837800-102843800	Weak transcription	Aorta	Aorta
12	chr8:102838600-102848400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr8:102839600-102843800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr8:102840400-102843400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr8:102840400-102843800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr8:102840400-102843800	Weak transcription	Left Ventricle	heart
17	chr8:102840400-102843800	Weak transcription	NHDF-Ad	bronchial
18	chr8:102840400-102844000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr8:102840400-102844200	Weak transcription	HSMMtube	muscle
20	chr8:102840400-102844400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr8:102840600-102843800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr8:102840600-102844000	Weak transcription	Fetal Muscle Leg	muscle
23	chr8:102840600-102844200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr8:102840800-102845200	Weak transcription	Adipose Nuclei	Adipose

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