Variant report

Variant	rs2165580
Chromosome Location	chr3:140355273-140355274
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1070466	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1441874	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1441876	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466847	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1494522	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1494523	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1494524	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1494525	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1494527	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1494528	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1499874	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1499875	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1499876	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1540506	0.86[CEU][hapmap]
rs16850633	0.83[EUR][1000 genomes]
rs1690852	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1690853	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1690856	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1690857	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1690863	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1690864	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1690865	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1690879	0.87[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1696194	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1696196	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1696197	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1696199	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1696200	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1696201	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1696219	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1706546	0.86[EUR][1000 genomes]
rs1837862	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2583808	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs347967	0.82[EUR][1000 genomes]
rs55895318	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs696577	0.83[EUR][1000 genomes]
rs696578	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs698657	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs698660	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs698662	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs698663	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs698664	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs698665	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs698666	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs698668	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs698669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs698670	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs698671	0.81[AMR][1000 genomes]
rs698672	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs698675	0.86[CEU][hapmap]
rs698676	0.80[EUR][1000 genomes]
rs698677	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs702278	0.86[EUR][1000 genomes]
rs836929	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs837661	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs863903	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs967669	0.86[EUR][1000 genomes]
rs967670	0.86[EUR][1000 genomes]
rs9843100	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757891	chr3:139925764-140524730	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2759181	chr3:139925764-140524730	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv527831	chr3:139932966-140533823	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv34489	chr3:140009020-140469302	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2757012	chr3:140009220-140460228	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv870185	chr3:140265153-140395673	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv877546	chr3:140299603-140468370	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv997694	chr3:140324012-140464786	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1008123	chr3:140328825-140464786	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv460869	chr3:140330108-140450655	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv591864	chr3:140330108-140450655	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv818170	chr3:140330108-140454836	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv829742	chr3:140334045-140357105	Enhancers Weak transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140350000-140355400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr3:140350200-140355400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:140350200-140355400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:140350200-140355400	Weak transcription	NH-A	brain
5	chr3:140350200-140355400	Weak transcription	NHEK	skin
6	chr3:140350400-140355400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:140353800-140356000	Enhancers	Placenta	Placenta
8	chr3:140354600-140355400	Enhancers	HepG2	liver
9	chr3:140354600-140355800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:140355000-140356000	Enhancers	NHDF-Ad	bronchial
11	chr3:140355000-140356200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:140355000-140356200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr3:140355000-140356600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:140355200-140355400	Flanking Active TSS	Osteobl	bone
15	chr3:140355200-140355800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:140355200-140355800	Enhancers	H9 Cell Line	embryonic stem cell
17	chr3:140355200-140355800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr3:140355200-140355800	Enhancers	Adipose Nuclei	Adipose
19	chr3:140355200-140355800	Enhancers	Fetal Muscle Leg	muscle
20	chr3:140355200-140355800	Enhancers	Ovary	ovary
21	chr3:140355200-140355800	Enhancers	Placenta Amnion	Placenta Amnion
22	chr3:140355200-140355800	Enhancers	HSMMtube	muscle
23	chr3:140355200-140356000	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr3:140355200-140356000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:140355200-140356000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:140355200-140356000	Enhancers	HMEC	breast
27	chr3:140355200-140356000	Enhancers	HSMM	muscle
28	chr3:140355200-140356200	Enhancers	HUVEC	blood vessel

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