Variant report

Variant	rs10506279
Chromosome Location	chr12:48703119-48703120
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48699980..48703428-chr12:48704506..48706488,3	K562	blood:
2	chr12:48702764..48705017-chr12:48706552..48708449,2	K562	blood:
3	chr12:48688262..48692290-chr12:48702214..48707293,5	K562	blood:
4	chr12:48698712..48702509-chr12:48702715..48705745,3	MCF-7	breast:

Extended variants
information (count: 94 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1004746	1.00[ASW][hapmap];0.92[CEU][hapmap]
rs10506276	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10506277	0.85[CEU][hapmap]
rs10506278	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10506280	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11830378	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs11830617	1.00[YRI][hapmap]
rs11830864	0.89[AMR][1000 genomes]
rs11833380	0.89[AMR][1000 genomes]
rs11834109	0.85[CEU][hapmap];0.95[EUR][1000 genomes]
rs11835938	1.00[ASN][1000 genomes]
rs11837419	0.89[AMR][1000 genomes]
rs11837548	0.89[AMR][1000 genomes]
rs11837571	0.89[AMR][1000 genomes]
rs12301562	1.00[ASN][1000 genomes]
rs17122906	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17122918	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs17122920	0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs17224674	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs17224828	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs17225198	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs17225261	0.81[CEU][hapmap]
rs17225751	0.85[CEU][hapmap]
rs17226359	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17226506	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17226723	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17823193	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs17823313	0.81[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs17823415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs17823565	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs17824200	0.82[EUR][1000 genomes]
rs17824705	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17824989	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17825013	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2450995	1.00[ASN][1000 genomes]
rs41291963	1.00[ASN][1000 genomes]
rs41291967	1.00[ASN][1000 genomes]
rs55638557	0.89[AMR][1000 genomes]
rs55654871	0.89[AMR][1000 genomes]
rs55684363	0.88[EUR][1000 genomes]
rs55763362	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55794326	0.82[EUR][1000 genomes]
rs55820056	1.00[ASN][1000 genomes]
rs55854069	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55920439	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56048326	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56084718	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56110736	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56271815	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56378318	0.88[EUR][1000 genomes]
rs56383074	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56389692	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56412095	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57956448	1.00[ASN][1000 genomes]
rs58317398	1.00[ASN][1000 genomes]
rs59724592	0.88[EUR][1000 genomes]
rs60209369	1.00[ASN][1000 genomes]
rs60679254	1.00[ASN][1000 genomes]
rs6580666	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7138353	0.89[AMR][1000 genomes]
rs7297558	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs7301153	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs7301509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs7307383	0.89[AMR][1000 genomes]
rs7307676	0.89[AMR][1000 genomes]
rs7307874	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs7310715	0.89[AMR][1000 genomes]
rs7310935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs73304917	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74089110	1.00[ASN][1000 genomes]
rs74089159	1.00[ASN][1000 genomes]
rs74089163	1.00[ASN][1000 genomes]
rs751315	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs751316	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7966782	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv899062	chr12:48658212-48711867	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv899063	chr12:48664989-48713768	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv899064	chr12:48664989-48721832	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv899065	chr12:48667019-48711867	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv899066	chr12:48667019-48713768	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	esv34952	chr12:48672333-48703533	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv469369	chr12:48675783-48711867	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv469370	chr12:48675783-48711867	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	nsv469372	chr12:48675783-48711867	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	nsv470290	chr12:48675783-48711867	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	nsv558791	chr12:48675783-48711867	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
18	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
19	nsv826362	chr12:48693048-48768853	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10506279	LOC255411	cis	cerebellum	SCAN
rs10506279	ZNF641	cis	multi-tissue	Pritchard
rs10506279	NCKAP5L	cis	parietal	SCAN
rs10506279	ZNF641	cis	Whole Blood	GTEx
rs10506279	DDN	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48699800-48705000	Weak transcription	Fetal Heart	heart
2	chr12:48701200-48704000	Weak transcription	K562	blood
3	chr12:48702800-48703800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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