Variant report

Variant	rs6074
Chromosome Location	chr15:58860963-58860964
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:58860510..58864232-chr15:58873033..58877399,5	K562	blood:
2	chr15:58860633..58862696-chr15:58874289..58877097,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11071391	0.87[CEU][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes]
rs11071393	0.86[TSI][hapmap]
rs12437457	1.00[ASW][hapmap];0.88[CEU][hapmap];0.81[GIH][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap]
rs12438487	0.82[CEU][hapmap]
rs12439231	0.82[CEU][hapmap]
rs12441313	0.82[CEU][hapmap]
rs12442451	0.82[CEU][hapmap]
rs12594742	0.82[CEU][hapmap]
rs12901989	0.88[CEU][hapmap]
rs12906714	0.82[CEU][hapmap]
rs12908261	0.82[CEU][hapmap]
rs12908645	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12913969	0.94[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap];0.82[EUR][1000 genomes]
rs12917577	0.88[CEU][hapmap]
rs16940587	0.87[CEU][hapmap]
rs16940589	0.88[CEU][hapmap]
rs16940647	0.82[CEU][hapmap]
rs16940651	0.82[CEU][hapmap]
rs17236194	1.00[ASW][hapmap];0.82[CEU][hapmap]
rs17301857	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17301864	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2242063	0.94[CEU][hapmap];0.81[CHB][hapmap];0.85[YRI][hapmap];0.82[EUR][1000 genomes]
rs2242066	0.94[CEU][hapmap];0.81[CHB][hapmap];0.82[EUR][1000 genomes]
rs2305421	0.88[CEU][hapmap]
rs28427123	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28455654	0.85[TSI][hapmap]
rs28458188	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28515698	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28524122	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28569241	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28602186	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36017602	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62005260	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6494030	0.82[CEU][hapmap]
rs6494033	0.82[CEU][hapmap]
rs6494034	0.81[CEU][hapmap]
rs7165035	0.82[CEU][hapmap]
rs7165402	0.82[CEU][hapmap]
rs7166076	0.82[CEU][hapmap]
rs7166325	0.82[CEU][hapmap]
rs7170314	0.82[CEU][hapmap]
rs7174386	0.81[CEU][hapmap]
rs7174414	0.86[CEU][hapmap]
rs8029805	0.82[CEU][hapmap]
rs8033691	0.82[CEU][hapmap]
rs8036005	0.88[CEU][hapmap]
rs8039791	0.80[GIH][hapmap]
rs871804	1.00[ASW][hapmap];0.94[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9302203	0.82[CEU][hapmap]
rs9635351	0.88[CEU][hapmap]
rs9920720	0.82[CEU][hapmap]
rs9921024	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1043041	chr15:58744505-58876327	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv569601	chr15:58800766-58866156	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1050231	chr15:58848727-58863526	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1043560	chr15:58851369-58863526	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6074	HSP90AB4P	cis	cerebellum	SCAN
rs6074	PIGB	cis	cerebellum	SCAN
rs6074	RNF111	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58853200-58865000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr15:58854600-58864200	Weak transcription	HepG2	liver
3	chr15:58854800-58868400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:58857800-58862800	Weak transcription	Colonic Mucosa	Colon
5	chr15:58859000-58865600	Weak transcription	Liver	Liver
6	chr15:58859800-58861000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr15:58859800-58861200	Enhancers	K562	blood
8	chr15:58860200-58861000	Enhancers	HUVEC	blood vessel
9	chr15:58860200-58861000	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr15:58860200-58861000	Enhancers	NHEK	skin
11	chr15:58860200-58861200	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr15:58860200-58861200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr15:58860200-58861200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:58860400-58861000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:58860400-58861000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr15:58860400-58861000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr15:58860400-58861000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr15:58860400-58861000	Enhancers	Dnd41	blood
19	chr15:58860400-58861200	Enhancers	Primary T cells from cord blood	blood
20	chr15:58860400-58861200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr15:58860400-58861200	Enhancers	Brain Anterior Caudate	brain
22	chr15:58860400-58861200	Enhancers	GM12878-XiMat	blood
23	chr15:58860600-58861800	Weak transcription	Pancreas	Pancrea
24	chr15:58860800-58863800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:58860800-58864800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr15:58860800-58865600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr15:58860800-58865600	Weak transcription	Fetal Thymus	thymus
28	chr15:58860800-58865800	Weak transcription	Stomach Mucosa	stomach
29	chr15:58860800-58866000	Weak transcription	Thymus	Thymus

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