Variant report

Variant	rs10887829
Chromosome Location	chr10:90259437-90259438
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10509544	0.85[AMR][1000 genomes]
rs10736353	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10736355	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10788597	0.81[CEU][hapmap]
rs10788601	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10788604	0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10788605	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10887827	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1177587	0.97[ASN][1000 genomes]
rs1183901	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12266064	0.95[MEX][hapmap];0.87[AMR][1000 genomes]
rs12778446	0.80[CHB][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1325903	0.88[ASW][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.98[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs1325907	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.88[MKK][hapmap];1.00[ASN][1000 genomes]
rs1359580	0.86[CHB][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs1409134	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1952122	0.83[ASW][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes]
rs2077890	1.00[ASN][1000 genomes]
rs2153856	0.84[ASW][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2437871	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs2437872	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2437874	0.87[ASN][1000 genomes]
rs2437877	0.98[ASN][1000 genomes]
rs2437878	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MKK][hapmap];0.96[ASN][1000 genomes]
rs2477952	0.85[CHB][hapmap]
rs2477955	0.96[ASN][1000 genomes]
rs2477957	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2488271	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2576166	0.85[CHB][hapmap]
rs2576174	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[ASN][1000 genomes]
rs2576179	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2576180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2765442	0.87[ASN][1000 genomes]
rs2765444	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2986118	0.86[ASN][1000 genomes]
rs6586130	0.83[AMR][1000 genomes]
rs7075544	0.91[AFR][1000 genomes]
rs7077182	0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7096710	0.94[ASW][hapmap];0.80[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs725683	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs725684	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs745354	0.86[CHB][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes]
rs7895199	0.83[AMR][1000 genomes]
rs7902230	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7907866	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7913372	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7917100	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs7919420	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7922053	0.85[AMR][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10887829	BTAF1	cis	cerebellum	SCAN
rs10887829	RNLS	cis	cerebellum	SCAN
rs10887829	LIPM	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90254000-90259600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr10:90254200-90259600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr10:90254200-90259600	Weak transcription	NHDF-Ad	bronchial
4	chr10:90255800-90259800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr10:90256000-90259800	Weak transcription	Fetal Kidney	kidney
6	chr10:90256000-90260000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr10:90257200-90259800	Weak transcription	Fetal Lung	lung
8	chr10:90257400-90260000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr10:90258200-90267200	Weak transcription	Adipose Nuclei	Adipose
10	chr10:90258400-90260600	Enhancers	Hela-S3	cervix
11	chr10:90258800-90259600	Enhancers	Fetal Thymus	thymus
12	chr10:90258800-90260200	Enhancers	Ovary	ovary
13	chr10:90258800-90260400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr10:90258800-90260600	Enhancers	HMEC	breast
15	chr10:90259000-90259600	Enhancers	Thymus	Thymus
16	chr10:90259000-90260400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr10:90259200-90259800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr10:90259200-90260400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr10:90259200-90260600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr10:90259200-90260600	Enhancers	NHEK	skin
21	chr10:90259400-90259600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr10:90259400-90260000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr10:90259400-90260000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr10:90259400-90260200	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr10:90259400-90260200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr10:90259400-90260400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr10:90259400-90260400	Enhancers	NH-A	brain
28	chr10:90259400-90260600	Enhancers	HSMM	muscle
29	chr10:90259400-90260600	Enhancers	Osteobl	bone

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