Variant report

Variant	rs865264
Chromosome Location	chr6:80639790-80639791
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:80638236..80641054-chr6:80645863..80647445,2	K562	blood:
2	chr6:80637410..80640151-chr6:80643092..80644970,2	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1007416	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.99[ASN][1000 genomes]
rs13191201	0.97[ASN][1000 genomes]
rs13199685	0.97[ASN][1000 genomes]
rs13201038	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs13207287	0.99[ASN][1000 genomes]
rs13216035	0.97[ASN][1000 genomes]
rs1398161	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1398162	0.96[ASN][1000 genomes]
rs1398163	0.99[ASN][1000 genomes]
rs1398164	0.99[ASN][1000 genomes]
rs1512118	0.99[ASN][1000 genomes]
rs151666	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs151667	1.00[ASN][1000 genomes]
rs151669	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs151671	0.81[JPT][hapmap];0.97[ASN][1000 genomes]
rs16891260	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.99[ASN][1000 genomes]
rs1742475	1.00[ASN][1000 genomes]
rs2322554	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs239517	0.97[ASN][1000 genomes]
rs239520	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs239521	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs239523	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239524	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239526	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239527	1.00[ASN][1000 genomes]
rs239528	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239529	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs239532	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2991	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.99[ASN][1000 genomes]
rs343618	1.00[ASN][1000 genomes]
rs343620	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs343623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs343627	1.00[ASN][1000 genomes]
rs343628	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs343629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343632	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343693	0.96[ASN][1000 genomes]
rs343694	0.96[ASN][1000 genomes]
rs343696	0.96[ASN][1000 genomes]
rs343697	0.96[ASN][1000 genomes]
rs343698	0.96[ASN][1000 genomes]
rs343699	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs343705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35163932	0.98[ASN][1000 genomes]
rs36067513	0.99[ASN][1000 genomes]
rs3812153	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.99[ASN][1000 genomes]
rs4706819	0.99[ASN][1000 genomes]
rs6454139	0.99[ASN][1000 genomes]
rs6915142	0.89[CHB][hapmap]
rs6928446	0.99[ASN][1000 genomes]
rs71565059	0.99[ASN][1000 genomes]
rs7743696	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.99[ASN][1000 genomes]
rs7754628	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[ASN][1000 genomes]
rs7754984	0.97[ASN][1000 genomes]
rs7770586	0.98[ASN][1000 genomes]
rs9443725	0.97[ASN][1000 genomes]
rs9443726	0.97[ASN][1000 genomes]
rs9448853	0.97[ASN][1000 genomes]
rs9448857	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9448858	0.99[ASN][1000 genomes]
rs9448861	0.99[ASN][1000 genomes]
rs9448862	0.99[ASN][1000 genomes]
rs9448863	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1032347	chr6:80284809-80694778	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv3475140	chr6:80592690-80679283	Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv3475142	chr6:80592789-80679132	Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv525646	chr6:80637239-80640847	Weak transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs865264	LCA5	cis	cerebellum	SCAN
rs865264	ELOVL4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80618400-80656000	Weak transcription	Aorta	Aorta
2	chr6:80622000-80643800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:80622000-80644200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:80624000-80643000	Weak transcription	NHDF-Ad	bronchial
5	chr6:80629200-80639800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr6:80630800-80639800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:80630800-80639800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:80631000-80653000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:80632000-80654800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:80633000-80646400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:80634800-80651000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:80637800-80641600	Enhancers	Dnd41	blood
13	chr6:80638400-80639800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr6:80638400-80651000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:80638800-80653000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:80639000-80640200	Enhancers	H1 Cell Line	embryonic stem cell
17	chr6:80639200-80642400	Weak transcription	Thymus	Thymus
18	chr6:80639400-80643200	Weak transcription	Fetal Thymus	thymus
19	chr6:80639600-80640400	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr6:80639600-80640400	Enhancers	HUES64 Cell Line	embryonic stem cell

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