Variant report

Variant	rs2607109
Chromosome Location	chr3:138395761-138395762
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs11705762	0.89[ASN][1000 genomes]
rs11709768	0.89[ASN][1000 genomes]
rs11713049	0.89[ASN][1000 genomes]
rs11720178	0.89[ASN][1000 genomes]
rs11924814	0.89[ASN][1000 genomes]
rs13082808	0.89[ASN][1000 genomes]
rs1400266	0.89[ASN][1000 genomes]
rs1663556	0.89[ASN][1000 genomes]
rs187245	0.89[ASN][1000 genomes]
rs191713	0.89[ASN][1000 genomes]
rs191714	0.89[ASN][1000 genomes]
rs2197387	0.89[ASN][1000 genomes]
rs244380	0.89[ASN][1000 genomes]
rs2595930	0.89[ASN][1000 genomes]
rs2595932	0.89[ASN][1000 genomes]
rs2607108	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28376988	0.89[ASN][1000 genomes]
rs28408150	0.89[ASN][1000 genomes]
rs34900559	1.00[ASN][1000 genomes]
rs35214574	0.89[ASN][1000 genomes]
rs361054	0.89[ASN][1000 genomes]
rs361055	0.89[ASN][1000 genomes]
rs361056	0.89[ASN][1000 genomes]
rs361059	0.89[ASN][1000 genomes]
rs361060	0.89[ASN][1000 genomes]
rs361062	0.89[ASN][1000 genomes]
rs361063	0.89[ASN][1000 genomes]
rs361064	0.89[ASN][1000 genomes]
rs361065	0.89[ASN][1000 genomes]
rs361066	0.89[ASN][1000 genomes]
rs361067	0.89[ASN][1000 genomes]
rs361068	0.89[ASN][1000 genomes]
rs361071	0.89[ASN][1000 genomes]
rs361072	0.89[ASN][1000 genomes]
rs361079	0.89[ASN][1000 genomes]
rs361080	0.89[ASN][1000 genomes]
rs361081	0.89[ASN][1000 genomes]
rs361082	0.89[ASN][1000 genomes]
rs361083	0.89[ASN][1000 genomes]
rs361084	0.89[ASN][1000 genomes]
rs361085	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361094	0.89[ASN][1000 genomes]
rs361096	0.89[ASN][1000 genomes]
rs361097	0.89[ASN][1000 genomes]
rs371762	0.89[ASN][1000 genomes]
rs385254	0.89[ASN][1000 genomes]
rs398065	0.89[ASN][1000 genomes]
rs404110	0.89[ASN][1000 genomes]
rs409507	0.89[ASN][1000 genomes]
rs413147	0.89[ASN][1000 genomes]
rs4305444	0.89[ASN][1000 genomes]
rs473388	0.89[ASN][1000 genomes]
rs476800	0.89[ASN][1000 genomes]
rs482334	0.89[ASN][1000 genomes]
rs4894350	0.89[ASN][1000 genomes]
rs4894351	0.89[ASN][1000 genomes]
rs4894352	0.89[ASN][1000 genomes]
rs4894353	0.89[ASN][1000 genomes]
rs4894354	0.89[ASN][1000 genomes]
rs493152	0.89[ASN][1000 genomes]
rs497900	0.89[ASN][1000 genomes]
rs500687	0.89[ASN][1000 genomes]
rs524164	0.89[ASN][1000 genomes]
rs531577	0.89[ASN][1000 genomes]
rs539619	0.89[ASN][1000 genomes]
rs540198	0.89[ASN][1000 genomes]
rs558905	0.89[ASN][1000 genomes]
rs564455	0.89[ASN][1000 genomes]
rs574942	0.89[ASN][1000 genomes]
rs589986	0.89[ASN][1000 genomes]
rs601032	0.84[AMR][1000 genomes]
rs607044	0.89[ASN][1000 genomes]
rs62282169	0.89[ASN][1000 genomes]
rs6439817	0.89[ASN][1000 genomes]
rs6776585	0.89[ASN][1000 genomes]
rs6781914	0.89[ASN][1000 genomes]
rs6801207	0.89[ASN][1000 genomes]
rs7612106	0.89[ASN][1000 genomes]
rs7641106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7643722	0.89[ASN][1000 genomes]
rs9821694	0.89[ASN][1000 genomes]
rs9822714	0.89[ASN][1000 genomes]
rs9832012	0.89[ASN][1000 genomes]
rs9834963	0.89[ASN][1000 genomes]
rs9864176	0.89[ASN][1000 genomes]
rs9874723	0.89[ASN][1000 genomes]
rs9879784	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv591854	chr3:138348081-138764229	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1010514	chr3:138365640-138737688	Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138360800-138407600	Weak transcription	HUVEC	blood vessel
2	chr3:138364400-138459200	Weak transcription	Psoas Muscle	Psoas
3	chr3:138368800-138400200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:138368800-138422600	Weak transcription	Right Atrium	heart
5	chr3:138369000-138493000	Weak transcription	Fetal Lung	lung
6	chr3:138369200-138401600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:138369200-138412800	Weak transcription	Hela-S3	cervix
8	chr3:138369200-138428800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:138369200-138435600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:138374800-138397000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:138375200-138429000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:138383000-138404800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:138383200-138412800	Weak transcription	Ovary	ovary
14	chr3:138383200-138448200	Weak transcription	Gastric	stomach
15	chr3:138383400-138426400	Weak transcription	Spleen	Spleen
16	chr3:138383400-138443000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:138383800-138400200	Weak transcription	Fetal Kidney	kidney
18	chr3:138383800-138405400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:138384000-138395800	Weak transcription	Fetal Stomach	stomach
20	chr3:138385000-138396200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:138385000-138418400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr3:138388400-138399600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:138389200-138401200	Weak transcription	Brain Substantia Nigra	brain
24	chr3:138389200-138405000	Weak transcription	Small Intestine	intestine
25	chr3:138390800-138459600	Weak transcription	Right Ventricle	heart
26	chr3:138391200-138422000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr3:138392200-138395800	ZNF genes & repeats	GM12878-XiMat	blood
28	chr3:138392200-138405600	Weak transcription	Stomach Mucosa	stomach
29	chr3:138392400-138396200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:138392400-138396400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:138392400-138396400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:138392600-138395800	Strong transcription	Liver	Liver
33	chr3:138392600-138397400	Strong transcription	Fetal Thymus	thymus
34	chr3:138392800-138395800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:138393000-138395800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
36	chr3:138393000-138395800	Strong transcription	Stomach Smooth Muscle	stomach
37	chr3:138393000-138396000	ZNF genes & repeats	Dnd41	blood
38	chr3:138393200-138395800	Weak transcription	Lung	lung
39	chr3:138393200-138396200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:138393200-138397200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:138393200-138399600	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr3:138393200-138401000	Weak transcription	Brain Angular Gyrus	brain
43	chr3:138393200-138405600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr3:138393200-138407800	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr3:138393400-138396200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:138393400-138399800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:138393600-138396200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
48	chr3:138393600-138396600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
49	chr3:138393600-138400200	Weak transcription	HepG2	liver
50	chr3:138393600-138405600	Weak transcription	HSMM	muscle

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