Variant report

Variant	rs1085617
Chromosome Location	chr3:120036705-120036706
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10048964	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1085614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1085616	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147681	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1147688	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1147689	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1147690	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1147697	0.81[AMR][1000 genomes]
rs11914405	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11928731	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13318758	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13318838	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13327125	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1625178	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1716855	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1716856	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1733326	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1733328	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2638597	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28535957	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28826066	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6764516	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6767308	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6777979	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6799005	0.86[AMR][1000 genomes]
rs6808913	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs787186	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787187	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787189	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787193	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787196	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787200	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787205	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs787206	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs787207	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs787208	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs809792	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923729	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs951658	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9810151	0.81[AMR][1000 genomes]
rs9810784	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9822636	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9822759	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9851711	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9856670	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9860676	0.81[AMR][1000 genomes]
rs9876547	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120024400-120049200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:120025400-120040600	Weak transcription	Fetal Lung	lung
3	chr3:120026600-120042400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:120026600-120060800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:120026800-120049200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:120026800-120067200	Weak transcription	Aorta	Aorta
7	chr3:120030000-120042600	Weak transcription	HMEC	breast
8	chr3:120031000-120041200	Weak transcription	Fetal Stomach	stomach
9	chr3:120031000-120042400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:120031000-120055600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:120031400-120040600	Weak transcription	Ovary	ovary
12	chr3:120031400-120042400	Weak transcription	A549	lung
13	chr3:120032400-120047600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:120032800-120042400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:120033000-120042200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:120033000-120042800	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:120033200-120044400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:120033200-120050000	Weak transcription	Spleen	Spleen
19	chr3:120033200-120060400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:120033200-120060400	Weak transcription	Pancreas	Pancrea
21	chr3:120033200-120067000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:120033600-120041000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:120034600-120052400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr3:120035000-120040200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:120035200-120049800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr3:120035800-120043000	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr3:120036400-120040200	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr3:120036400-120041600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:120036600-120053600	Weak transcription	Fetal Heart	heart

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