Variant report

Variant	rs871804
Chromosome Location	chr15:58844214-58844215
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:58843977..58845847-chr15:58846386..58849270,2	MCF-7	breast:
2	chr15:58844000..58845908-chr15:58853129..58855286,2	K562	blood:
3	chr15:58808761..58811985-chr15:58842114..58844975,3	K562	blood:
4	chr15:58841313..58844294-chr15:58848370..58850226,2	K562	blood:
5	chr15:58812575..58815325-chr15:58843755..58846624,5	K562	blood:
6	chr15:58838998..58841145-chr15:58842509..58846691,3	MCF-7	breast:
7	chr15:58836656..58842196-chr15:58843431..58849915,8	K562	blood:
8	chr15:58812575..58816304-chr15:58843755..58846624,5	K562	blood:
9	chr15:58545760..58547993-chr15:58842385..58845023,2	MCF-7	breast:
10	chr15:58843959..58845583-chr15:58846564..58848827,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000259476	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11071391	0.81[CEU][hapmap];0.82[YRI][hapmap]
rs12437457	1.00[ASW][hapmap];0.82[CEU][hapmap];0.96[MKK][hapmap];0.85[YRI][hapmap]
rs12901989	0.82[CEU][hapmap]
rs12908645	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12913969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12917577	0.82[CEU][hapmap]
rs16940587	0.82[CEU][hapmap]
rs16940589	0.82[CEU][hapmap]
rs17236194	1.00[ASW][hapmap]
rs17301857	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17301864	0.94[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2242063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242064	0.84[JPT][hapmap]
rs2242066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2305421	0.82[CEU][hapmap]
rs28427123	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28458188	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28515698	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28524122	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28569241	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28602186	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36017602	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6074	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]
rs62005260	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7174414	0.80[CEU][hapmap]
rs8036005	0.82[CEU][hapmap]
rs9635351	0.82[CEU][hapmap]
rs9921024	0.82[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	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3362898	chr15:58705732-58850860	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	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
6	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs871804	HSP90AB4P	cis	cerebellum	SCAN
rs871804	RNF111	cis	parietal	SCAN
rs871804	PIGB	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58829000-58847600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:58837000-58848400	Enhancers	Fetal Thymus	thymus
3	chr15:58838000-58845000	Enhancers	Placenta	Placenta
4	chr15:58838200-58845600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr15:58838800-58845000	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr15:58839200-58845200	Enhancers	Placenta Amnion	Placenta Amnion
7	chr15:58839800-58844400	Weak transcription	Ovary	ovary
8	chr15:58839800-58844400	Weak transcription	Spleen	Spleen
9	chr15:58840200-58844800	Strong transcription	Liver	Liver
10	chr15:58840600-58849200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:58840800-58845600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:58840800-58849600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:58841800-58844600	Weak transcription	Fetal Brain Male	brain
14	chr15:58842400-58844600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr15:58842600-58845600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:58842600-58846200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr15:58842800-58844400	Enhancers	GM12878-XiMat	blood
18	chr15:58842800-58845600	Enhancers	Dnd41	blood
19	chr15:58843200-58846200	Enhancers	Thymus	Thymus
20	chr15:58843400-58844400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:58843400-58844400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr15:58843400-58844400	Enhancers	Colonic Mucosa	Colon
23	chr15:58843400-58844600	Enhancers	Primary T cells from cord blood	blood
24	chr15:58843400-58844600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
25	chr15:58843400-58844600	Enhancers	Primary hematopoietic stem cells	blood
26	chr15:58843400-58844600	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr15:58843400-58844600	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr15:58843400-58844600	Enhancers	A549	lung
29	chr15:58843400-58844600	Flanking Active TSS	Osteobl	bone
30	chr15:58843400-58845200	Enhancers	Fetal Intestine Large	intestine
31	chr15:58843400-58846400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr15:58843600-58844400	Weak transcription	Lung	lung
33	chr15:58843600-58844600	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr15:58843600-58844800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:58843600-58845200	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr15:58843800-58844400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr15:58843800-58844400	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr15:58843800-58844600	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr15:58843800-58844600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:58843800-58844600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr15:58843800-58844600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr15:58843800-58844600	Enhancers	Esophagus	oesophagus
43	chr15:58843800-58844600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
44	chr15:58843800-58844600	Enhancers	Fetal Kidney	kidney
45	chr15:58843800-58844600	Flanking Active TSS	K562	blood
46	chr15:58843800-58844600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr15:58843800-58844600	Flanking Active TSS	NH-A	brain
48	chr15:58843800-58844800	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr15:58843800-58844800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr15:58843800-58844800	Flanking Active TSS	HepG2	liver

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