Variant report

Variant	rs17566917
Chromosome Location	chr5:75625274-75625275
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr5:75625273-75625510	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:75624448..75626842-chr5:75628180..75631008,2	K562	blood:

Variant related genes	Relation type
ENSG00000266045	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs17651829	1.00[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs31266	0.95[ASN][1000 genomes]
rs31269	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer 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
2	nsv870415	chr5:75526088-75738412	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1032033	chr5:75609686-75646482	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1023310	chr5:75609686-75651786	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv3353515	chr5:75609996-75632294	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv3425598	chr5:75610980-75647048	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv2757120	chr5:75611597-75642974	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv2759352	chr5:75611597-75642974	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1028669	chr5:75611597-75643598	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1020853	chr5:75611597-75651786	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv598678	chr5:75614737-75628413	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17566917	TNPO1	cis	parietal	SCAN
rs17566917	ZBED3	cis	cerebellum	SCAN
rs17566917	ANKRA2	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75620400-75629400	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr5:75620600-75627000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr5:75620600-75629600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr5:75620600-75630400	Enhancers	Primary hematopoietic stem cells	blood
5	chr5:75621000-75626800	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr5:75621400-75627800	Weak transcription	Pancreas	Pancrea
7	chr5:75621600-75627000	Weak transcription	Fetal Intestine Small	intestine
8	chr5:75621800-75627000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr5:75622000-75625600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr5:75622000-75627000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr5:75622000-75627000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr5:75622000-75629800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:75622200-75625400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr5:75622200-75629000	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr5:75622400-75626800	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr5:75622400-75627600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr5:75622600-75626200	Weak transcription	Primary B cells from cord blood	blood
18	chr5:75622600-75626800	Weak transcription	Adipose Nuclei	Adipose
19	chr5:75622600-75627200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr5:75622600-75633600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:75622800-75627200	Weak transcription	Dnd41	blood
22	chr5:75622800-75627400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr5:75622800-75634000	Weak transcription	Esophagus	oesophagus
24	chr5:75623200-75626200	Weak transcription	HepG2	liver
25	chr5:75623200-75627000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:75623200-75627000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:75623200-75627000	Weak transcription	Fetal Muscle Leg	muscle
28	chr5:75623200-75627000	Weak transcription	Placenta	Placenta
29	chr5:75623200-75627000	Weak transcription	Thymus	Thymus
30	chr5:75623200-75627400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr5:75623200-75627400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:75623200-75628000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr5:75623200-75628600	Weak transcription	Fetal Lung	lung
34	chr5:75623200-75628800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr5:75623400-75627400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr5:75623600-75626200	Weak transcription	Brain Anterior Caudate	brain
37	chr5:75623800-75627200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr5:75624000-75625600	Weak transcription	Primary T cells from cord blood	blood
39	chr5:75624000-75627400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr5:75624000-75629600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr5:75624400-75626800	Weak transcription	Fetal Thymus	thymus
42	chr5:75624400-75627000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr5:75624400-75627000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr5:75624400-75627200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr5:75624400-75627400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr5:75624600-75626200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr5:75624600-75626800	Weak transcription	Fetal Stomach	stomach
48	chr5:75624600-75627000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr5:75624600-75627000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr5:75624600-75629600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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