Variant report

Variant	rs4263729
Chromosome Location	chr8:105566722-105566723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:105565492..105567421-chr8:105600088..105601868,2	MCF-7	breast:
2	chr8:105565178..105567381-chr8:105597153..105599899,2	K562	blood:
3	chr8:105564767..105567386-chr8:105599921..105602701,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147650	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10505062	0.83[CEU][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes]
rs10955352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11777528	0.83[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs11782865	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11782889	0.95[AFR][1000 genomes]
rs11783651	0.81[CEU][hapmap]
rs11784193	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs11989936	0.83[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs11995774	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11996303	0.93[AFR][1000 genomes]
rs12677524	1.00[JPT][hapmap]
rs12678904	0.83[CEU][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes]
rs12678962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12680250	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12681898	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13249169	1.00[JPT][hapmap]
rs13250948	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs13259268	0.81[AFR][1000 genomes]
rs13264598	1.00[JPT][hapmap]
rs13265309	0.83[CEU][hapmap]
rs13266321	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13266739	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs13268122	1.00[JPT][hapmap]
rs13268597	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13279448	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs16871500	0.94[ASW][hapmap];0.83[CEU][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs16871634	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2028244	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28481880	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3018438	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34255383	0.82[AFR][1000 genomes]
rs35328383	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35465370	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35649342	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4236775	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4338071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4593510	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs4734803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59294667	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6468939	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67712332	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6984152	0.80[AFR][1000 genomes]
rs6990243	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs6993149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6994764	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs7004507	0.88[ASW][hapmap];0.83[CEU][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];0.80[AFR][1000 genomes]
rs7010576	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71520892	0.83[AFR][1000 genomes]
rs7465442	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7815871	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7821181	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs7823671	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7834086	0.88[ASW][hapmap];0.83[CEU][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes]
rs7841202	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7842204	0.81[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs7845137	0.83[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs9694676	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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	nsv1016087	chr8:105228670-105934368	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1026754	chr8:105382508-106030916	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv539709	chr8:105382508-106030916	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv831417	chr8:105455814-105625608	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
5	nsv508522	chr8:105532034-105614403	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4263729	LRP12	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:105521800-105568800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:105557400-105583800	Weak transcription	Thymus	Thymus
3	chr8:105565600-105568000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr8:105565800-105566800	Weak transcription	Ovary	ovary
5	chr8:105566000-105575800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr8:105566200-105573000	Weak transcription	K562	blood
7	chr8:105566200-105587200	Weak transcription	Left Ventricle	heart
8	chr8:105566400-105568000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr8:105566400-105583400	Weak transcription	Fetal Thymus	thymus
10	chr8:105566600-105568000	ZNF genes & repeats	Dnd41	blood

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