Variant report

Variant	rs17423232
Chromosome Location	chr3:111400162-111400163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:111400111-111400685	A549	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:111394548..111396118-chr3:111400082..111401919,2	MCF-7	breast:
2	chr3:111393572..111395550-chr3:111399941..111402074,2	MCF-7	breast:
3	chr3:111393069..111396445-chr3:111398541..111400605,3	K562	blood:
4	chr3:111386277..111388195-chr3:111399221..111401634,2	MCF-7	breast:
5	chr3:111393603..111396498-chr3:111398541..111400894,4	K562	blood:

No data

Variant related genes	Relation type
PLCXD2-AS1	TF binding region
ENSG00000240766	Chromatin interaction
ENSG00000240891	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs17281311	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17488681	0.94[CEU][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17488841	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3733176	0.81[TSI][hapmap]
rs6770144	0.81[TSI][hapmap]
rs73228199	0.81[AMR][1000 genomes]
rs73230104	0.81[AMR][1000 genomes]
rs73230106	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73230108	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73230114	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73230118	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73230122	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73230126	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73230140	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73230146	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73230153	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73230160	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73230168	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17423232	ZNF80	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111394000-111401400	Weak transcription	Aorta	Aorta
2	chr3:111394200-111403600	Weak transcription	Pancreas	Pancrea
3	chr3:111395400-111400400	Weak transcription	Esophagus	oesophagus
4	chr3:111395400-111403600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:111395800-111413400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:111396400-111400400	Weak transcription	HepG2	liver
7	chr3:111396400-111401600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:111396400-111406800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:111396400-111408200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:111396600-111400400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:111396600-111400400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:111396600-111400400	Weak transcription	Stomach Mucosa	stomach
13	chr3:111396600-111409200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:111397000-111400200	Weak transcription	Thymus	Thymus
15	chr3:111397000-111400400	Weak transcription	HMEC	breast
16	chr3:111397000-111403200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr3:111397000-111403600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:111397000-111403600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:111397000-111404800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr3:111397200-111400200	Weak transcription	Primary B cells from cord blood	blood
21	chr3:111397200-111400200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:111397200-111400200	Weak transcription	A549	lung
23	chr3:111397200-111400200	Weak transcription	Hela-S3	cervix
24	chr3:111397200-111408000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr3:111397200-111408200	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:111398600-111400600	Enhancers	GM12878-XiMat	blood
27	chr3:111398800-111401200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:111399000-111400600	Genic enhancers	Primary T cells from cord blood	blood
29	chr3:111399000-111409400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr3:111399600-111401200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:111399600-111401400	Enhancers	Duodenum Mucosa	Duodenum
32	chr3:111399800-111401000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:111399800-111401200	Enhancers	NHEK	skin
34	chr3:111399800-111401600	Enhancers	Fetal Intestine Large	intestine
35	chr3:111399800-111401800	Enhancers	Fetal Intestine Small	intestine
36	chr3:111400000-111400400	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr3:111400000-111400800	Enhancers	Small Intestine	intestine
38	chr3:111400000-111400800	Enhancers	HSMMtube	muscle
39	chr3:111400000-111401000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:111400000-111401000	Enhancers	Fetal Thymus	thymus
41	chr3:111400000-111401200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr3:111400000-111401400	Enhancers	Primary B cells from peripheral blood	blood
43	chr3:111400000-111401400	Enhancers	Rectal Mucosa Donor 31	rectum

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