Variant report

Variant	rs10461657
Chromosome Location	chr5:58277992-58277993
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58266429..58269015-chr5:58276417..58278899,2	K562	blood:
2	chr5:58277726..58280597-chr5:58283029..58284667,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10074854	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1463816	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1498612	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1532520	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1553114	1.00[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs159724	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1846369	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1973450	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1973451	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2927661	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2936190	0.93[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs2936193	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs2936199	0.89[EUR][1000 genomes]
rs2968006	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs2968013	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2968014	0.93[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2968015	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2968017	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3805553	0.93[CEU][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3805554	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3805556	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3805557	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs412423	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4321723	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs457959	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4621516	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4629551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699930	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699931	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4700314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6450496	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6875727	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs702519	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs702523	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7712725	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7713069	0.93[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7713345	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7724713	0.93[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7737685	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830312	chr5:58191579-58382226	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10461657	PDE4D	cis	lymphoblastoid	seeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58266000-58287600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr5:58266800-58281200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:58267600-58280000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:58267600-58282600	Strong transcription	Primary T cells from cord blood	blood
5	chr5:58268000-58278000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:58268000-58281800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:58268000-58288400	Weak transcription	Stomach Mucosa	stomach
8	chr5:58268200-58280400	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr5:58268200-58287200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:58268400-58287400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr5:58268400-58294400	Weak transcription	NH-A	brain
12	chr5:58268600-58279400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:58268600-58279600	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr5:58268800-58280000	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr5:58268800-58280200	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr5:58268800-58286000	Weak transcription	HepG2	liver
17	chr5:58268800-58286600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr5:58268800-58286800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr5:58268800-58287200	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr5:58268800-58287800	Weak transcription	Placenta	Placenta
21	chr5:58268800-58288800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr5:58268800-58294600	Weak transcription	Brain Hippocampus Middle	brain
23	chr5:58269000-58279400	Strong transcription	Primary hematopoietic stem cells	blood
24	chr5:58269200-58279400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:58270200-58297400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr5:58270400-58279200	Weak transcription	Fetal Kidney	kidney
27	chr5:58270800-58292600	Weak transcription	Fetal Brain Male	brain
28	chr5:58270800-58295800	Weak transcription	Small Intestine	intestine
29	chr5:58270800-58297000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:58271000-58278000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr5:58271000-58282000	Genic enhancers	A549	lung
32	chr5:58271000-58283000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr5:58271000-58283600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr5:58271000-58285800	Weak transcription	Aorta	Aorta
35	chr5:58271000-58285800	Weak transcription	Pancreas	Pancrea
36	chr5:58271000-58287600	Weak transcription	Esophagus	oesophagus
37	chr5:58271000-58293600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr5:58271000-58294600	Weak transcription	Brain Angular Gyrus	brain
39	chr5:58271600-58278000	Weak transcription	Fetal Stomach	stomach
40	chr5:58271600-58278000	Weak transcription	Gastric	stomach
41	chr5:58271600-58278200	Weak transcription	Spleen	Spleen
42	chr5:58271600-58278800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr5:58271600-58287200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:58271600-58294400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr5:58271800-58281200	Weak transcription	Fetal Intestine Small	intestine
46	chr5:58272000-58279000	Weak transcription	Liver	Liver
47	chr5:58272000-58281000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr5:58272200-58286000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr5:58272400-58283800	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr5:58272800-58278200	Weak transcription	Primary B cells from cord blood	blood

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