Variant report

Variant	rs3860823
Chromosome Location	chr6:150356526-150356527
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:150351052..150353254-chr6:150355645..150357982,2	K562	blood:
2	chr6:150354931..150357925-chr6:150386556..150388661,2	K562	blood:
3	chr6:150354901..150357527-chr6:150362159..150364156,2	MCF-7	breast:
4	chr6:150355810..150358323-chr6:150360175..150362251,2	K562	blood:

Variant related genes	Relation type
ENSG00000235972	Chromatin interaction
ENSG00000213091	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10155731	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11155696	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11155697	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11752529	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11752629	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11754987	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11757186	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12204988	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13198863	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13209192	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs1543547	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1853664	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34006533	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4086064	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5006620	0.93[CHB][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5017314	0.83[EUR][1000 genomes]
rs5017315	0.83[EUR][1000 genomes]
rs5017316	0.86[EUR][1000 genomes]
rs562425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs563278	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61730071	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72561813	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs763574	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9478354	0.85[EUR][1000 genomes]
rs9478362	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9478380	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9479403	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9479404	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9479405	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9479429	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9479478	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9479481	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9479482	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9479513	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv7375	chr6:150324114-150388625	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3344440	chr6:150324131-150388650	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3323918	chr6:150327978-150392099	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv886766	chr6:150335407-150364009	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv886767	chr6:150335407-150400488	Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv464077	chr6:150338065-150358012	Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv604847	chr6:150338065-150358012	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv5535	chr6:150339697-150361659	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv886768	chr6:150340035-150366143	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv886769	chr6:150346037-150364009	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3860823	UST	cis	cerebellum	SCAN
rs3860823	LATS1	cis	cerebellum	SCAN
rs3860823	C6orf72	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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