Variant report

Variant	rs16870224
Chromosome Location	chr5:40692940-40692941
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:39589555..39591618-chr5:40691990..40693771,2	MCF-7	breast:

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs16870378	0.87[CHB][hapmap];0.96[CHD][hapmap]
rs3792822	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.80[TSI][hapmap]
rs3805486	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.80[TSI][hapmap]
rs4432939	0.91[ASN][1000 genomes]
rs4957341	0.94[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6451534	0.90[ASN][1000 genomes]
rs6887174	0.83[JPT][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	nsv880539	chr5:40662257-40713645	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16870224	PTGER4	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40684000-40700600	Weak transcription	Left Ventricle	heart
2	chr5:40684600-40700400	Weak transcription	Right Ventricle	heart
3	chr5:40688200-40693800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
4	chr5:40688400-40696400	Weak transcription	Liver	Liver
5	chr5:40688400-40700400	Weak transcription	Stomach Mucosa	stomach
6	chr5:40688800-40694600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr5:40688800-40696800	Weak transcription	Fetal Lung	lung
8	chr5:40688800-40697000	Strong transcription	Fetal Thymus	thymus
9	chr5:40688800-40718600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:40689600-40693000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr5:40689600-40694400	Strong transcription	Primary hematopoietic stem cells	blood
12	chr5:40690000-40695800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:40690200-40693000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
14	chr5:40690200-40693200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr5:40690200-40694200	Weak transcription	Osteobl	bone
16	chr5:40690200-40694600	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr5:40690200-40695200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr5:40690400-40693000	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr5:40690400-40695200	Strong transcription	HSMM	muscle
20	chr5:40690400-40697200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr5:40690600-40693000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:40690600-40695400	Strong transcription	Duodenum Mucosa	Duodenum
23	chr5:40690800-40694200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr5:40690800-40694800	Strong transcription	HUVEC	blood vessel
25	chr5:40690800-40695800	Weak transcription	A549	lung
26	chr5:40691200-40694600	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr5:40691200-40694800	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr5:40691200-40695200	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr5:40691200-40697000	Strong transcription	Primary T cells from cord blood	blood
30	chr5:40691400-40695000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr5:40691600-40693000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr5:40691600-40693000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr5:40691600-40693000	Strong transcription	Fetal Muscle Trunk	muscle
34	chr5:40691600-40693000	Strong transcription	Rectal Smooth Muscle	rectum
35	chr5:40691600-40693000	Strong transcription	NHEK	skin
36	chr5:40691600-40693600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr5:40691600-40695200	Strong transcription	Adipose Nuclei	Adipose
38	chr5:40691600-40695400	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr5:40691800-40693000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr5:40691800-40693000	Strong transcription	Fetal Intestine Large	intestine
41	chr5:40691800-40693000	Strong transcription	HMEC	breast
42	chr5:40691800-40693600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr5:40692000-40693800	Strong transcription	NH-A	brain
44	chr5:40692200-40693000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr5:40692200-40693000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:40692200-40701800	Weak transcription	Colon Smooth Muscle	Colon
47	chr5:40692400-40693000	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr5:40692400-40694200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr5:40692400-40695200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr5:40692400-40741200	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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