Variant report

Variant	rs2105001
Chromosome Location	chr10:116693443-116693444
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr10:116693368-116693711	MCF10A-Er-Src	breast:	n/a	chr10:116693518-116693528 chr10:116693518-116693527 chr10:116693518-116693528 chr10:116693518-116693528 chr10:116693518-116693528
2	MAFK	chr10:116693413-116693600	IMR90	lung:	n/a	n/a
3	STAT3	chr10:116693040-116693691	MCF10A-Er-Src	breast:	n/a	chr10:116693560-116693568 chr10:116693558-116693569
4	FOS	chr10:116693332-116693691	MCF10A-Er-Src	breast:	n/a	chr10:116693518-116693528 chr10:116693518-116693527 chr10:116693518-116693528 chr10:116693518-116693528 chr10:116693518-116693528
5	MYC	chr10:116693418-116693668	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr10:116693384-116693737	MCF10A-Er-Src	breast:	n/a	chr10:116693560-116693568 chr10:116693558-116693569
7	STAT3	chr10:116693382-116693731	MCF10A-Er-Src	breast:	n/a	chr10:116693560-116693568 chr10:116693558-116693569
8	FOS	chr10:116693331-116693736	MCF10A-Er-Src	breast:	n/a	chr10:116693518-116693528 chr10:116693518-116693527 chr10:116693518-116693528 chr10:116693518-116693528 chr10:116693518-116693528
9	STAT3	chr10:116693399-116693737	MCF10A-Er-Src	breast:	n/a	chr10:116693560-116693568 chr10:116693558-116693569
10	FOS	chr10:116693331-116693740	MCF10A-Er-Src	breast:	n/a	chr10:116693518-116693528 chr10:116693518-116693527 chr10:116693518-116693528 chr10:116693518-116693528 chr10:116693518-116693528
11	E2F4	chr10:116693432-116693744	MCF10A-Er-Src	breast:	n/a	n/a
12	MYC	chr10:116693339-116693618	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:116691563..116693571-chr10:116695644..116697264,2	MCF-7	breast:

Variant related genes	Relation type
TRUB1	TF binding region

Extended variants
information (count: 108 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10160015	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10444099	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1045657	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10490908	1.00[JPT][hapmap]
rs10510008	0.86[ASN][1000 genomes]
rs10885631	0.82[ASN][1000 genomes]
rs10885632	0.86[ASN][1000 genomes]
rs10885633	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10885634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885636	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885637	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10885638	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10885639	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11196983	0.86[ASN][1000 genomes]
rs11196984	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11196989	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11196991	1.00[ASN][1000 genomes]
rs11196996	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11196999	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11197000	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11197005	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11197006	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11197007	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11197010	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11197011	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11197012	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11197023	0.95[ASN][1000 genomes]
rs12098332	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12246008	0.95[ASN][1000 genomes]
rs12265048	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12269261	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12761122	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12764662	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12772737	0.95[ASN][1000 genomes]
rs12774597	0.95[ASN][1000 genomes]
rs12775180	1.00[JPT][hapmap]
rs12779231	0.95[ASN][1000 genomes]
rs17092542	1.00[JPT][hapmap]
rs17721283	1.00[JPT][hapmap]
rs17721905	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17722042	0.95[ASN][1000 genomes]
rs17794346	1.00[JPT][hapmap]
rs17795104	0.95[ASN][1000 genomes]
rs17795212	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1966384	1.00[JPT][hapmap]
rs2095379	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420070	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34170154	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs34434610	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs34453431	0.95[ASN][1000 genomes]
rs34461950	0.87[ASN][1000 genomes]
rs35501899	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs35811923	0.95[ASN][1000 genomes]
rs3931556	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61869271	0.95[ASN][1000 genomes]
rs61869272	0.95[ASN][1000 genomes]
rs61869274	0.95[ASN][1000 genomes]
rs61869275	0.95[ASN][1000 genomes]
rs6585302	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6585306	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6585309	0.91[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.83[MEX][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6585310	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6585311	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[ASN][1000 genomes]
rs6585313	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7071789	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[ASN][1000 genomes]
rs7071812	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7072356	1.00[JPT][hapmap]
rs7074729	1.00[JPT][hapmap]
rs7075888	1.00[JPT][hapmap]
rs7077170	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7079234	0.95[ASN][1000 genomes]
rs7085964	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7086663	0.83[ASW][hapmap];0.81[CEU][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.86[YRI][hapmap]
rs7093282	0.83[ASN][1000 genomes]
rs7093330	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7094072	1.00[JPT][hapmap]
rs7097580	0.95[ASN][1000 genomes]
rs7099565	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099590	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7099779	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100026	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7100159	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100894	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72836518	0.95[ASN][1000 genomes]
rs749649	1.00[JPT][hapmap]
rs7895551	1.00[JPT][hapmap]
rs7898249	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7904605	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7908069	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7908464	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7909566	1.00[JPT][hapmap]
rs7909657	1.00[JPT][hapmap]
rs7917523	0.96[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7923295	1.00[JPT][hapmap]
rs881192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951585	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs968848	0.95[ASN][1000 genomes]
rs968849	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv831996	chr10:116601552-116772968	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv1039002	chr10:116643095-116879483	Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv2761634	chr10:116643095-116879495	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription 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	10 gene(s)	inside rSNPs	diseases
8	nsv1045654	chr10:116654574-116879483	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv1043242	chr10:116655057-116883386	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv831997	chr10:116689552-116855698	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2105001	TRUB1	Cis_1M	lymphoblastoid	RTeQTL
rs2105001	GFRA1	cis	parietal	SCAN
rs2105001	C10orf84	cis	cerebellum	SCAN
rs2105001	ADRB1	cis	parietal	SCAN
rs2105001	TRUB1	cis	cerebellum	SCAN
rs2105001	TRUB1	cis	parietal	SCAN
rs2105001	EMX2	cis	cerebellum	SCAN
rs2105001	ATRNL1	cis	Muscle Skeletal	GTEx
rs2105001	TECTB	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116691800-116697800	Weak transcription	Pancreas	Pancrea
2	chr10:116692400-116697600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr10:116692800-116693800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr10:116692800-116693800	Enhancers	Hela-S3	cervix
5	chr10:116693000-116693800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr10:116693000-116693800	Enhancers	Muscle Satellite Cultured Cells	--
7	chr10:116693000-116693800	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr10:116693000-116693800	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr10:116693000-116693800	Enhancers	HMEC	breast
10	chr10:116693000-116693800	Enhancers	Osteobl	bone
11	chr10:116693000-116694000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr10:116693000-116694000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr10:116693000-116694200	Enhancers	NHEK	skin
14	chr10:116693200-116693800	Enhancers	Psoas Muscle	Psoas
15	chr10:116693200-116693800	Enhancers	HSMMtube	muscle
16	chr10:116693200-116694000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr10:116693200-116694200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr10:116693400-116693800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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