Variant report

Variant	rs2302782
Chromosome Location	chr17:66446803-66446804
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr17:66446559-66446963	T-47D	breast:	n/a	n/a
2	GATA3	chr17:66446483-66447043	T-47D	breast:	n/a	n/a
3	POLR2A	chr17:66446297-66446965	HepG2	liver:	n/a	n/a
4	FOXA1	chr17:66446568-66446930	T-47D	breast:	n/a	n/a
5	GATA3	chr17:66446533-66446937	T-47D	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:66437281..66438931-chr17:66445313..66446855,2	K562	blood:
2	chr17:66444999..66447953-chr17:66450443..66453876,4	K562	blood:
3	chr17:66285931..66287761-chr17:66445684..66448003,2	MCF-7	breast:
4	chr17:66445448..66449611-chr17:66450414..66454852,7	K562	blood:
5	chr17:66253563..66256097-chr17:66446212..66449080,2	MCF-7	breast:

No data

Variant related genes	Relation type
WIPI1	TF binding region
ENSG00000108932	Chromatin interaction
ENSG00000070540	Chromatin interaction
ENSG00000141337	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11656906	1.00[ASW][hapmap];0.83[CEU][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs12940626	0.85[CEU][hapmap]
rs12943181	0.87[ASW][hapmap]
rs1808333	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2287301	0.87[CEU][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2909212	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2909214	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2952278	1.00[ASW][hapmap];0.86[YRI][hapmap]
rs2952291	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71378929	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs869657	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs883620	0.85[EUR][1000 genomes]
rs918167	1.00[ASW][hapmap];0.87[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][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	nsv833523	chr17:66343323-66510461	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2302782	PITPNC1	cis	cerebellum	SCAN
rs2302782	WIPI1	cis	parietal	SCAN
rs2302782	WIPI1	cis	lymphoblastoid	seeQTL
rs2302782	CD79B	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66410400-66452400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:66420800-66451800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr17:66425400-66451600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:66425400-66452000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr17:66432200-66452400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr17:66432600-66451600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr17:66432800-66448200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr17:66433000-66451800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr17:66433000-66451800	Weak transcription	Hela-S3	cervix
10	chr17:66434400-66447800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr17:66434400-66450200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr17:66434600-66449000	Weak transcription	Thymus	Thymus
13	chr17:66434600-66450400	Strong transcription	Osteobl	bone
14	chr17:66434800-66452200	Weak transcription	Dnd41	blood
15	chr17:66434800-66452400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr17:66434800-66452600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr17:66435200-66452200	Weak transcription	Stomach Mucosa	stomach
18	chr17:66435600-66449400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr17:66435800-66447600	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr17:66436000-66449000	Strong transcription	NHLF	lung
21	chr17:66437200-66447000	Strong transcription	HepG2	liver
22	chr17:66437200-66451600	Weak transcription	GM12878-XiMat	blood
23	chr17:66437400-66451600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr17:66437400-66451600	Weak transcription	Small Intestine	intestine
25	chr17:66437600-66452800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr17:66437800-66448000	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr17:66437800-66448200	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr17:66437800-66449200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr17:66438000-66449200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr17:66438000-66452000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr17:66438200-66449000	Weak transcription	Primary T cells from cord blood	blood
32	chr17:66438200-66449800	Weak transcription	Fetal Lung	lung
33	chr17:66438200-66452000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr17:66438200-66452000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr17:66438200-66452400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr17:66438400-66447200	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr17:66438400-66447800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr17:66438400-66452400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr17:66438400-66452400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr17:66438600-66449200	Strong transcription	Lung	lung
41	chr17:66438800-66448600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr17:66438800-66449400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr17:66439000-66447800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr17:66439000-66450400	Weak transcription	Primary B cells from cord blood	blood
45	chr17:66439200-66447600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr17:66439200-66449400	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr17:66439600-66449400	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr17:66439800-66447200	Strong transcription	Adipose Nuclei	Adipose
49	chr17:66439800-66448000	Strong transcription	HSMMtube	muscle
50	chr17:66440200-66449000	Strong transcription	Stomach Smooth Muscle	stomach

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