Variant report

Variant	rs4541958
Chromosome Location	chr8:118926059-118926060
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:118924992..118927722-chr8:118950419..118952468,2	MCF-7	breast:

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10087446	0.87[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap]
rs10097196	0.87[CEU][hapmap];0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs10105797	0.86[ASN][1000 genomes]
rs10106675	0.83[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10808489	0.81[JPT][hapmap]
rs10955841	0.80[EUR][1000 genomes]
rs10955846	0.87[CEU][hapmap]
rs1125103	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11774623	0.87[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11776458	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11777220	0.96[ASN][1000 genomes]
rs11777874	0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs11780699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11781153	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11781245	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11783359	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11784409	0.87[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11784466	0.82[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12682332	0.82[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13252084	0.82[CEU][hapmap]
rs13256042	0.83[CEU][hapmap]
rs13260665	0.87[CEU][hapmap]
rs1462985	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1466429	0.87[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap]
rs1542519	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1564132	0.83[CEU][hapmap]
rs17430540	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17430610	0.83[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17450835	0.87[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17450856	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17450863	0.86[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17450876	0.87[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17452966	0.87[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17453043	0.83[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17475190	0.83[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17479600	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2008799	0.87[CEU][hapmap]
rs2199545	0.87[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap]
rs2219724	0.87[CEU][hapmap]
rs2447535	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2447536	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2447537	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2447538	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2447539	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2447540	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2447541	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2514719	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2514720	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28357271	0.87[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28357275	0.83[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28357276	0.87[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28357277	0.83[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3101574	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3860883	0.84[CEU][hapmap];0.85[GIH][hapmap]
rs4298514	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs4391466	0.83[CEU][hapmap];0.91[CHB][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4467961	0.80[CEU][hapmap];0.85[GIH][hapmap]
rs4480148	0.86[TSI][hapmap]
rs4602926	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4621831	0.86[TSI][hapmap]
rs4644291	0.99[EUR][1000 genomes]
rs4876771	0.84[CEU][hapmap]
rs4876774	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs4876775	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs4876777	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4876781	0.87[CEU][hapmap]
rs4876782	0.87[CEU][hapmap];0.87[CHD][hapmap]
rs4876783	0.87[CEU][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap]
rs4876784	0.83[CEU][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap]
rs5005135	0.83[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56748438	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62521139	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62521140	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62521141	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6469716	0.87[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6469718	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs6982505	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6985552	0.87[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6997503	0.81[JPT][hapmap]
rs6999044	0.83[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7007735	0.87[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7012890	0.87[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7812722	0.91[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs7820452	0.87[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7822297	0.82[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7824327	0.87[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7824391	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7824395	0.87[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7824651	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7836747	0.87[CEU][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7840309	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs7842917	0.86[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7843515	0.87[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs958381	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9643120	0.87[CEU][hapmap]
rs9656923	0.83[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9656925	0.83[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019636	chr8:118598433-118946091	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv539734	chr8:118598433-118946091	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv933516	chr8:118764605-119009093	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1030459	chr8:118840179-119155835	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv831440	chr8:118871930-119052269	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv891411	chr8:118891896-118942698	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1032355	chr8:118896733-119003223	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv465785	chr8:118901928-118970300	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv612046	chr8:118901928-118970300	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4541958	NOBOX	trans	multi-tissue	Pritchard

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:118919000-118926800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr8:118919200-118933200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr8:118921200-118926400	Enhancers	NHDF-Ad	bronchial
4	chr8:118921200-118926600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr8:118921600-118926400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr8:118921800-118926400	Enhancers	NHLF	lung
7	chr8:118922400-118926400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr8:118922800-118932800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr8:118922800-118934800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr8:118923000-118926600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr8:118923200-118926400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr8:118923200-118926400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr8:118923200-118933000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr8:118923600-118926800	Enhancers	Osteobl	bone
15	chr8:118923800-118930000	Weak transcription	Pancreas	Pancrea
16	chr8:118923800-118933800	Weak transcription	Fetal Stomach	stomach
17	chr8:118924000-118932800	Weak transcription	Ovary	ovary
18	chr8:118924000-118933000	Weak transcription	Lung	lung
19	chr8:118924800-118926400	Enhancers	HSMM	muscle
20	chr8:118924800-118926600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr8:118925000-118926400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr8:118925000-118927000	Weak transcription	Liver	Liver
23	chr8:118925000-118927800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr8:118925400-118926400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr8:118925400-118926400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr8:118925400-118926400	Enhancers	HMEC	breast
27	chr8:118925600-118926200	Enhancers	Colon Smooth Muscle	Colon
28	chr8:118925600-118926400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr8:118925600-118926400	Enhancers	NH-A	brain
30	chr8:118925800-118926200	Weak transcription	Aorta	Aorta
31	chr8:118925800-118926400	Enhancers	A549	lung
32	chr8:118925800-118926400	Enhancers	NHEK	skin
33	chr8:118925800-118926600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr8:118925800-118926600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr8:118926000-118928800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr8:118926000-118931600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr8:118926000-118932800	Weak transcription	HSMMtube	muscle

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