Variant report

Variant	rs10519565
Chromosome Location	chr4:141796795-141796796
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	chr4:141787778..141789643-chr4:141796789..141798752,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12499698	0.92[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12507690	0.93[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12509724	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12640427	0.81[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];0.81[TSI][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12641776	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12642343	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12649599	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2129645	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2220344	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4481296	0.93[CEU][hapmap];0.85[CHB][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4956335	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.86[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4956488	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55761420	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55784158	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56135301	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58594074	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59222460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60124370	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62344966	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62344969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62344971	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62344995	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62344996	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62344997	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6811265	0.93[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6819107	0.93[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6829424	0.93[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6829449	0.93[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6834848	0.93[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6835056	0.93[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72722313	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9799616	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880167	chr4:141616979-142092124	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv830090	chr4:141770494-141947764	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv1845859	chr4:141786475-141816657	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv830091	chr4:141796603-141980546	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10519565	NDUFC1	cis	cerebellum	SCAN
rs10519565	SETD7	cis	cerebellum	SCAN
rs10519565	GAB1	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:141778400-141797600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr4:141778600-141798000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr4:141789600-141797200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:141789600-141797200	Weak transcription	Colon Smooth Muscle	Colon
5	chr4:141789600-141831600	Weak transcription	Aorta	Aorta
6	chr4:141791800-141796800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:141792000-141797600	Weak transcription	Left Ventricle	heart
8	chr4:141792000-141797600	Weak transcription	Ovary	ovary
9	chr4:141792000-141797600	Weak transcription	Right Atrium	heart
10	chr4:141792000-141798800	Weak transcription	Right Ventricle	heart
11	chr4:141792000-141802800	Weak transcription	Gastric	stomach
12	chr4:141793000-141797000	Weak transcription	Fetal Stomach	stomach
13	chr4:141793200-141797200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr4:141793800-141797600	Weak transcription	Adipose Nuclei	Adipose
15	chr4:141795200-141799000	Enhancers	Fetal Heart	heart
16	chr4:141795200-141799200	Enhancers	Fetal Lung	lung
17	chr4:141795400-141798000	Enhancers	Fetal Muscle Leg	muscle
18	chr4:141796000-141798000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:141796200-141797800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr4:141796400-141796800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:141796400-141797800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:141796400-141797800	Enhancers	Brain Germinal Matrix	brain
23	chr4:141796400-141798000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:141796400-141798000	Enhancers	Fetal Brain Male	brain
25	chr4:141796400-141798200	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr4:141796400-141798400	Enhancers	Fetal Brain Female	brain
27	chr4:141796400-141798600	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr4:141796400-141799200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:141796600-141797800	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr4:141796600-141797800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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