Variant report

Variant	rs2589260
Chromosome Location	chr3:137772478-137772479
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1444577	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1444578	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2589259	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622705	0.81[JPT][hapmap]
rs2622713	0.96[ASN][1000 genomes]
rs2622724	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2622725	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2622726	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2622730	0.81[EUR][1000 genomes]
rs2622745	0.82[EUR][1000 genomes]
rs2724693	0.84[JPT][hapmap]
rs2724703	0.81[EUR][1000 genomes]
rs2724707	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs2724708	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs2724713	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2724717	0.81[EUR][1000 genomes]
rs2724720	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2724721	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2724722	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2724723	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs329382	0.82[EUR][1000 genomes]
rs329388	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs329389	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[EUR][1000 genomes]
rs329390	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[EUR][1000 genomes]
rs329391	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[EUR][1000 genomes]
rs365504	0.83[EUR][1000 genomes]
rs374045	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs382629	0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs389697	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs390729	0.81[EUR][1000 genomes]
rs405265	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs405517	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs405602	0.82[JPT][hapmap]
rs419075	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs425938	0.87[EUR][1000 genomes]
rs436145	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs445025	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs446644	0.82[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs453023	0.82[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9814877	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9834670	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv877535	chr3:137521204-137776539	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv2757890	chr3:137611789-137933835	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2759180	chr3:137611789-137933835	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv2751978	chr3:137715302-137890750	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1007857	chr3:137767454-137843106	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137729400-137780400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:137742000-137780200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:137744400-137792000	Weak transcription	Fetal Kidney	kidney
4	chr3:137749600-137780000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:137750000-137781800	Weak transcription	Lung	lung
6	chr3:137750600-137782200	Weak transcription	Fetal Intestine Small	intestine
7	chr3:137754400-137783000	Weak transcription	Stomach Mucosa	stomach
8	chr3:137763000-137780600	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:137763000-137797600	Weak transcription	Hela-S3	cervix
10	chr3:137763400-137780400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:137763400-137781400	Weak transcription	HSMMtube	muscle
12	chr3:137763400-137782600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:137763600-137778200	Weak transcription	HSMM	muscle
14	chr3:137766200-137781000	Weak transcription	NHEK	skin
15	chr3:137766400-137772600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:137766800-137774000	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr3:137766800-137780400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:137766800-137783600	Weak transcription	Brain Substantia Nigra	brain
19	chr3:137767000-137776000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:137767000-137778800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:137767000-137782800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:137767200-137791800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:137767400-137780400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:137767400-137780400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:137767600-137779600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:137768200-137773800	Weak transcription	Adipose Nuclei	Adipose
27	chr3:137768200-137777400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:137768200-137780000	Weak transcription	Spleen	Spleen
29	chr3:137768200-137782800	Weak transcription	Esophagus	oesophagus
30	chr3:137768200-137787600	Weak transcription	A549	lung
31	chr3:137768400-137777800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:137768400-137780400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr3:137768400-137782200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:137768600-137780000	Weak transcription	Aorta	Aorta
35	chr3:137768600-137782200	Weak transcription	Gastric	stomach
36	chr3:137768600-137783600	Weak transcription	Pancreas	Pancrea
37	chr3:137768800-137772600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:137768800-137772800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:137768800-137772800	Weak transcription	NH-A	brain
40	chr3:137768800-137778200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:137768800-137778200	Weak transcription	Left Ventricle	heart
42	chr3:137768800-137778800	Weak transcription	Fetal Stomach	stomach
43	chr3:137768800-137779000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:137768800-137779600	Weak transcription	NHDF-Ad	bronchial
45	chr3:137768800-137779600	Weak transcription	Osteobl	bone
46	chr3:137768800-137779800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:137768800-137779800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:137768800-137779800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:137768800-137779800	Weak transcription	Right Ventricle	heart
50	chr3:137768800-137781000	Weak transcription	Rectal Smooth Muscle	rectum

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