Variant report

Variant	rs725684
Chromosome Location	chr10:90259126-90259127
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10509551	0.90[LWK][hapmap]
rs10749586	0.81[CEU][hapmap];0.80[GIH][hapmap];0.96[MEX][hapmap];0.91[AMR][1000 genomes]
rs10749587	0.90[AMR][1000 genomes]
rs10749588	0.91[AMR][1000 genomes]
rs10788604	0.94[ASN][1000 genomes]
rs10788605	1.00[ASN][1000 genomes]
rs10887827	1.00[ASN][1000 genomes]
rs10887829	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10887831	0.92[LWK][hapmap]
rs11202750	0.85[CEU][hapmap];0.91[AMR][1000 genomes]
rs1177587	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1183901	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12778446	0.80[CHB][hapmap]
rs1325900	0.85[LWK][hapmap];0.85[YRI][hapmap]
rs1325903	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs1325906	0.85[LWK][hapmap];0.85[YRI][hapmap]
rs1325907	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359580	0.86[CHB][hapmap]
rs1409134	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17112571	0.85[YRI][hapmap]
rs17112575	0.85[YRI][hapmap]
rs1925937	0.94[AMR][1000 genomes]
rs1935578	0.81[CEU][hapmap];0.82[GIH][hapmap];0.96[MEX][hapmap];0.92[AMR][1000 genomes]
rs1952122	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs1980812	0.91[AMR][1000 genomes]
rs2077890	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2153856	0.89[CHD][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];0.85[ASN][1000 genomes]
rs2437871	0.82[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.94[AMR][1000 genomes]
rs2437872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2437874	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2437877	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2437878	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2477952	0.85[CHB][hapmap];0.92[AMR][1000 genomes]
rs2477955	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2477957	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2488271	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2576166	0.82[CEU][hapmap];0.85[CHB][hapmap];0.91[AMR][1000 genomes]
rs2576174	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs2576180	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2765441	0.88[AFR][1000 genomes]
rs2765442	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2765444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2986118	0.92[CEU][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4403718	0.91[AMR][1000 genomes]
rs4934414	0.85[YRI][hapmap]
rs7076491	0.81[YRI][hapmap]
rs725683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs745354	0.86[CHB][hapmap]
rs7902230	1.00[ASN][1000 genomes]
rs7904229	0.95[AMR][1000 genomes]
rs7916937	0.84[CEU][hapmap];0.91[AMR][1000 genomes]
rs7917100	0.95[CHB][hapmap];1.00[JPT][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	nsv482385	chr10:90066140-90259751	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv948664	chr10:90076715-90517150	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1054984	chr10:90122512-90278038	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1050587	chr10:90146582-90272627	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv540739	chr10:90146582-90272627	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv825500	chr10:90221443-90302503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv533167	chr10:90236197-90341481	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs725684	LIPM	cis	cerebellum	SCAN
rs725684	LIPA	cis	cerebellum	SCAN
rs725684	IFIT3	cis	parietal	SCAN
rs725684	CCNJ	trans	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90254000-90259400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr10:90254000-90259600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr10:90254200-90259200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr10:90254200-90259400	Weak transcription	Osteobl	bone
5	chr10:90254200-90259600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr10:90254200-90259600	Weak transcription	NHDF-Ad	bronchial
7	chr10:90255800-90259800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr10:90256000-90259800	Weak transcription	Fetal Kidney	kidney
9	chr10:90256000-90260000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr10:90256400-90259400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr10:90257200-90259800	Weak transcription	Fetal Lung	lung
12	chr10:90257400-90260000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr10:90258000-90259400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr10:90258200-90267200	Weak transcription	Adipose Nuclei	Adipose
15	chr10:90258400-90259400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr10:90258400-90260600	Enhancers	Hela-S3	cervix
17	chr10:90258800-90259600	Enhancers	Fetal Thymus	thymus
18	chr10:90258800-90260200	Enhancers	Ovary	ovary
19	chr10:90258800-90260400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr10:90258800-90260600	Enhancers	HMEC	breast
21	chr10:90259000-90259600	Enhancers	Thymus	Thymus
22	chr10:90259000-90260400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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