Variant report

Variant	rs8082254
Chromosome Location	chr17:66527460-66527461
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:66508255..66510518-chr17:66525854..66528774,2	K562	blood:

Variant related genes	Relation type
ENSG00000108946	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10468444	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10491176	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10852738	1.00[CEU][hapmap];0.85[CHD][hapmap];0.91[MEX][hapmap]
rs16972996	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16973034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2015212	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2302235	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3785905	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55736761	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56112060	0.80[ASN][1000 genomes]
rs7221724	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72847781	0.84[ASN][1000 genomes]
rs72847782	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72847784	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72847785	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72847787	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72847789	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72847790	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72847794	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72847801	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74000753	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8067357	0.80[ASN][1000 genomes]
rs8072598	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833524	chr17:66524030-66705194	Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8082254	WIPI1	cis	cerebellum	SCAN
rs8082254	SNORD104	cis	cerebellum	SCAN
rs8082254	PITPNC1	cis	cerebellum	SCAN
rs8082254	AMZ2P1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66511600-66537000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr17:66511600-66537000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr17:66511800-66531600	Strong transcription	Fetal Intestine Large	intestine
4	chr17:66511800-66536600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr17:66511800-66537000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr17:66511800-66537800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr17:66512000-66530000	Strong transcription	HSMM	muscle
8	chr17:66513200-66528600	Strong transcription	Muscle Satellite Cultured Cells	--
9	chr17:66513200-66533000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr17:66514200-66528800	Strong transcription	HepG2	liver
11	chr17:66514800-66527800	Strong transcription	Fetal Muscle Trunk	muscle
12	chr17:66514800-66537000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:66514800-66537400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr17:66514800-66537600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr17:66515000-66535800	Strong transcription	Placenta	Placenta
16	chr17:66515200-66533400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr17:66515200-66534600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr17:66516600-66535800	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr17:66516800-66535400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr17:66517200-66530000	Strong transcription	Osteobl	bone
21	chr17:66517200-66537600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr17:66517400-66537000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr17:66517600-66528800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr17:66517600-66529800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr17:66517600-66532200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr17:66517600-66535400	Strong transcription	HMEC	breast
27	chr17:66517600-66536800	Strong transcription	Fetal Thymus	thymus
28	chr17:66517600-66537200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr17:66517800-66528600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr17:66518000-66528200	Strong transcription	NHDF-Ad	bronchial
31	chr17:66518000-66534000	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr17:66518000-66534600	Strong transcription	A549	lung
33	chr17:66518000-66535800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr17:66518000-66536800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr17:66518000-66537200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr17:66518200-66527800	Strong transcription	Fetal Muscle Leg	muscle
37	chr17:66518200-66530000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr17:66518200-66534600	Strong transcription	Primary B cells from cord blood	blood
39	chr17:66518200-66536600	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr17:66518200-66536800	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr17:66518200-66537600	Strong transcription	Primary T cells from cord blood	blood
42	chr17:66518200-66537800	Strong transcription	Duodenum Mucosa	Duodenum
43	chr17:66518400-66527600	Strong transcription	NHLF	lung
44	chr17:66518400-66527800	Strong transcription	HSMMtube	muscle
45	chr17:66518400-66527800	Strong transcription	K562	blood
46	chr17:66518400-66532400	Strong transcription	Dnd41	blood
47	chr17:66518400-66533800	Strong transcription	Primary B cells from peripheral blood	blood
48	chr17:66518400-66534600	Strong transcription	GM12878-XiMat	blood
49	chr17:66518400-66535600	Strong transcription	Primary hematopoietic stem cells	blood
50	chr17:66518400-66535600	Strong transcription	Rectal Mucosa Donor 29	rectum

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