Variant report

Variant	rs4128461
Chromosome Location	chr1:71526710-71526711
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:71510894..71514340-chr1:71523075..71528309,6	K562	blood:

Variant related genes	Relation type
ENSG00000050628	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1009311	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10399704	0.80[EUR][1000 genomes]
rs10399705	0.80[EUR][1000 genomes]
rs10399706	0.80[EUR][1000 genomes]
rs10399797	0.80[EUR][1000 genomes]
rs10493481	1.00[CEU][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11209733	0.83[TSI][hapmap]
rs11209736	0.80[EUR][1000 genomes]
rs11209739	0.81[EUR][1000 genomes]
rs11209740	0.81[EUR][1000 genomes]
rs11209743	0.89[EUR][1000 genomes]
rs11209747	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12035210	0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs12118599	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12119958	0.84[EUR][1000 genomes]
rs12130153	0.83[TSI][hapmap]
rs12131265	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap]
rs12139565	0.94[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12139719	0.80[EUR][1000 genomes]
rs12139935	0.80[EUR][1000 genomes]
rs12729268	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12739047	0.80[EUR][1000 genomes]
rs12739685	0.83[EUR][1000 genomes]
rs12748649	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12756951	0.80[EUR][1000 genomes]
rs1983588	0.85[TSI][hapmap]
rs2066373	0.80[EUR][1000 genomes]
rs2268054	0.83[AFR][1000 genomes]
rs2268055	0.83[TSI][hapmap]
rs2268062	0.83[TSI][hapmap]
rs2300178	0.98[TSI][hapmap];0.80[EUR][1000 genomes]
rs2817864	0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs3765894	0.83[TSI][hapmap]
rs4397614	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4520371	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs4650099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4650100	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5682	0.83[TSI][hapmap]
rs7556111	0.96[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs8179367	0.80[EUR][1000 genomes]
rs8179390	0.83[TSI][hapmap]
rs8179408	0.80[EUR][1000 genomes]
rs880098	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs997997	0.83[TSI][hapmap]

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	nsv546472	chr1:71432984-71541003	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	555 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4128461	PTGER3	cis	uninvolved skin	skin_eQTL
rs4128461	PTGER3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:71513600-71533600	Weak transcription	Lung	lung
2	chr1:71514000-71527400	Weak transcription	Colon Smooth Muscle	Colon
3	chr1:71514000-71530600	Weak transcription	Ovary	ovary
4	chr1:71514000-71533600	Weak transcription	Pancreas	Pancrea
5	chr1:71514000-71533600	Weak transcription	Right Ventricle	heart
6	chr1:71514200-71533600	Weak transcription	Spleen	Spleen
7	chr1:71515800-71541000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:71519000-71530200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:71519200-71533400	Weak transcription	Fetal Intestine Small	intestine
10	chr1:71519400-71528200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:71519600-71528000	Weak transcription	Brain Germinal Matrix	brain
12	chr1:71520000-71536800	Weak transcription	Aorta	Aorta
13	chr1:71520400-71533600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:71520400-71534600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:71520600-71527200	Weak transcription	Fetal Kidney	kidney
16	chr1:71520600-71533600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:71520600-71544600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:71520800-71527400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:71521000-71529800	Weak transcription	Brain Angular Gyrus	brain
20	chr1:71521200-71533600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:71521400-71530400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:71521400-71544200	Strong transcription	Adipose Nuclei	Adipose
23	chr1:71521600-71528400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr1:71521600-71536800	Weak transcription	Stomach Mucosa	stomach
25	chr1:71521800-71530400	Weak transcription	Small Intestine	intestine
26	chr1:71521800-71544600	Strong transcription	HSMM	muscle
27	chr1:71522000-71528200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr1:71522000-71534400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:71522000-71543800	Strong transcription	Primary B cells from cord blood	blood
30	chr1:71522000-71544200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:71522000-71544200	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:71522000-71544200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:71522000-71544400	Strong transcription	HMEC	breast
34	chr1:71522200-71529000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:71522200-71532600	Strong transcription	GM12878-XiMat	blood
36	chr1:71522200-71534000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr1:71522200-71540800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:71522200-71544200	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr1:71522200-71544600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr1:71522400-71530200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr1:71522400-71544200	Strong transcription	Liver	Liver
42	chr1:71522600-71527400	Weak transcription	HepG2	liver
43	chr1:71522600-71532800	Strong transcription	Primary T cells from cord blood	blood
44	chr1:71522600-71533400	Weak transcription	Fetal Stomach	stomach
45	chr1:71522600-71544200	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr1:71522600-71544200	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr1:71522600-71544400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:71522600-71544400	Strong transcription	NH-A	brain
49	chr1:71522800-71540400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:71522800-71544400	Strong transcription	Fetal Thymus	thymus

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