Variant report

Variant	rs2080898
Chromosome Location	chr5:112314281-112314282
allele	C/T
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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:112255209..112259355-chr5:112310614..112316433,9	K562	blood:
2	chr5:112253961..112259306-chr5:112310933..112315767,8	K562	blood:
3	chr5:112313991..112316155-chr5:112326453..112328052,2	K562	blood:
4	chr5:112312938..112314772-chr5:112369842..112371988,2	K562	blood:
5	chr5:112255914..112262078-chr5:112308752..112315375,16	MCF-7	breast:
6	chr5:112312686..112316155-chr5:112325860..112328052,3	K562	blood:
7	chr5:112296171..112299064-chr5:112312877..112315865,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000129625	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10463645	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10478101	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10515453	1.00[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.83[ASN][1000 genomes]
rs13360862	0.82[MEX][hapmap]
rs1422222	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs1978430	0.82[CEU][hapmap]
rs2080899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3209874	0.91[CHB][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs3733968	0.90[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs4309965	0.90[JPT][hapmap]
rs57874459	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6594653	0.81[CEU][hapmap];0.93[EUR][1000 genomes]
rs66612320	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6865320	0.81[CHB][hapmap]
rs6876686	0.91[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs6879139	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6892784	0.91[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs6896598	0.81[CEU][hapmap]
rs7033	0.91[CHB][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap]
rs73229015	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7733267	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1019756	chr5:112242315-112325943	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1028759	chr5:112300490-112358514	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2080898	AQPEP	cis	parietal	SCAN
rs2080898	DCP2	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112311600-112314400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr5:112311600-112314800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:112311600-112315200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr5:112311800-112314400	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr5:112311800-112314600	Active TSS	Fetal Intestine Large	intestine
6	chr5:112311800-112314800	Active TSS	H1 Cell Line	embryonic stem cell
7	chr5:112311800-112315000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr5:112311800-112315200	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr5:112312000-112314400	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr5:112312000-112314400	Bivalent/Poised TSS	HepG2	liver
11	chr5:112312000-112314600	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr5:112312000-112314600	Active TSS	NHDF-Ad	bronchial
13	chr5:112312000-112314800	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr5:112312000-112314800	Active TSS	NHLF	lung
15	chr5:112312000-112315200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:112312000-112315200	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr5:112312000-112315400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:112312000-112315600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:112312000-112316000	Active TSS	K562	blood
20	chr5:112312200-112314400	Active TSS	Fetal Thymus	thymus
21	chr5:112312200-112314400	Active TSS	Thymus	Thymus
22	chr5:112312200-112314400	Active TSS	NHEK	skin
23	chr5:112312200-112314800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:112312200-112316600	Active TSS	GM12878-XiMat	blood
25	chr5:112312600-112315600	Active TSS	Right Atrium	heart
26	chr5:112313000-112314400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:112313000-112314800	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr5:112313000-112316400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr5:112313200-112314600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr5:112313200-112315400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr5:112313200-112315800	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr5:112313200-112329000	Weak transcription	Spleen	Spleen
33	chr5:112313400-112314600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr5:112313400-112314600	Active TSS	Brain Germinal Matrix	brain
35	chr5:112313400-112314800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr5:112313600-112314400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
37	chr5:112313600-112314600	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr5:112313600-112316400	Enhancers	Fetal Brain Male	brain
39	chr5:112313800-112314400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr5:112313800-112314600	Enhancers	Primary B cells from peripheral blood	blood
41	chr5:112313800-112314800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr5:112313800-112314800	Flanking Active TSS	Fetal Brain Female	brain
43	chr5:112313800-112315000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr5:112313800-112315000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:112313800-112315400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr5:112313800-112315600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:112313800-112315800	Flanking Active TSS	Dnd41	blood
48	chr5:112313800-112337600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr5:112314000-112314400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr5:112314000-112314400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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