Variant report

Variant	rs1889486
Chromosome Location	chr10:96184220-96184221
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	chr10:96174854..96177531-chr10:96183896..96185905,2	MCF-7	breast:

Extended variants
information (count: 111 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10786168	0.91[MEX][hapmap];0.86[TSI][hapmap]
rs10786169	0.83[YRI][hapmap]
rs1079504	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10882452	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10882454	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10882460	0.91[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10882463	0.91[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10882470	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10882474	0.91[MEX][hapmap];0.86[TSI][hapmap]
rs11187937	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11187939	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11187944	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11187948	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11187952	0.84[LWK][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11187958	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11187966	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11187972	0.83[EUR][1000 genomes]
rs11187973	0.86[EUR][1000 genomes]
rs11187980	0.83[ASW][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11187996	0.87[AFR][1000 genomes]
rs11187998	0.91[GIH][hapmap];0.85[JPT][hapmap]
rs11188005	0.86[EUR][1000 genomes]
rs11188009	0.83[ASW][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.84[TSI][hapmap];0.93[YRI][hapmap]
rs11188017	0.81[EUR][1000 genomes]
rs11188019	0.93[LWK][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs11188026	0.81[EUR][1000 genomes]
rs11188030	0.80[EUR][1000 genomes]
rs11188040	0.84[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs11527881	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11638	0.91[MEX][hapmap];0.82[TSI][hapmap]
rs12218213	0.84[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs12218216	0.84[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs12219906	0.84[CEU][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs12220588	0.84[CEU][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs12221475	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12573638	0.92[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs12762574	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1359263	0.84[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs1749352	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1749355	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1749356	0.85[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1889485	0.85[EUR][1000 genomes]
rs1889487	0.84[EUR][1000 genomes]
rs1969815	0.92[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs1977290	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1980741	0.84[EUR][1000 genomes]
rs2012670	0.82[AFR][1000 genomes]
rs2095380	0.84[EUR][1000 genomes]
rs2148553	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs2244241	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2265362	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2265364	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2274417	0.84[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs2281791	0.91[MEX][hapmap];0.86[TSI][hapmap]
rs2860760	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2860821	0.84[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs2901764	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2901765	0.82[EUR][1000 genomes]
rs35774063	0.87[EUR][1000 genomes]
rs3740358	0.91[MEX][hapmap];0.82[TSI][hapmap]
rs4316436	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4351744	0.91[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs4421688	0.80[EUR][1000 genomes]
rs4611135	0.92[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs479664	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4917505	0.80[EUR][1000 genomes]
rs4918333	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4918402	0.91[MEX][hapmap];0.82[TSI][hapmap]
rs4918403	0.82[EUR][1000 genomes]
rs4918409	0.92[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs4918417	0.84[CEU][hapmap]
rs4918419	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs493088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs517784	0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs522111	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs541704	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs542540	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs556055	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56020662	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs576517	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs581165	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6583943	0.81[EUR][1000 genomes]
rs6583944	0.92[CEU][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs6583945	0.81[EUR][1000 genomes]
rs692872	0.91[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs701885	0.91[MEX][hapmap];0.82[TSI][hapmap]
rs7073639	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7078236	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7078811	0.91[LWK][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap]
rs7083898	0.84[EUR][1000 genomes]
rs7086462	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7087472	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7089094	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7393251	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7898330	0.85[AFR][1000 genomes]
rs7906843	0.89[LWK][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs7906968	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs7913343	0.87[CEU][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7921721	0.83[ASW][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8181426	0.88[AFR][1000 genomes]
rs912466	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9420641	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs945123	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs955694	0.92[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes]
rs9633699	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761616	chr10:95966768-96303701	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv831946	chr10:96055190-96226438	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv1819509	chr10:96064300-96361776	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	esv1815355	chr10:96162545-96189900	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv1817623	chr10:96162545-96189900	Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1889486	HELLS	cis	cerebellum	SCAN
rs1889486	KIF11	cis	cerebellum	SCAN
rs1889486	C19orf22	trans	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96163800-96184400	Weak transcription	Gastric	stomach
2	chr10:96164800-96188200	Weak transcription	Right Atrium	heart
3	chr10:96171600-96188200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr10:96171800-96198200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr10:96173400-96188400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr10:96173600-96190200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr10:96180800-96184600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr10:96181400-96187800	Weak transcription	Brain Substantia Nigra	brain
9	chr10:96182600-96184400	Enhancers	Osteobl	bone
10	chr10:96182800-96186800	Weak transcription	Brain Hippocampus Middle	brain
11	chr10:96183000-96184600	Enhancers	HSMMtube	muscle
12	chr10:96183000-96191600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr10:96183200-96184800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr10:96183600-96188400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr10:96183800-96184600	Enhancers	Brain Cingulate Gyrus	brain
16	chr10:96183800-96184600	Enhancers	HSMM	muscle
17	chr10:96183800-96188200	Weak transcription	NH-A	brain
18	chr10:96184000-96184600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr10:96184200-96184400	Enhancers	Brain Anterior Caudate	brain
20	chr10:96184200-96188200	Weak transcription	Muscle Satellite Cultured Cells	--

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