Variant report

Variant	rs28870092
Chromosome Location	chr3:99813622-99813623
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10049383	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1017968	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11537816	0.83[AMR][1000 genomes]
rs13064704	0.82[AMR][1000 genomes]
rs13069311	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs13093838	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13323143	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1489816	0.82[AMR][1000 genomes]
rs17392948	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2291494	0.82[AMR][1000 genomes]
rs2291495	0.82[AMR][1000 genomes]
rs28714363	0.82[AMR][1000 genomes]
rs34996634	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35154249	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35669453	0.82[AMR][1000 genomes]
rs35844878	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35885423	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62285461	0.82[AMR][1000 genomes]
rs62285462	0.82[AMR][1000 genomes]
rs62285471	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62285473	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62285478	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6790877	0.82[AMR][1000 genomes]
rs6802422	0.82[AMR][1000 genomes]
rs7610486	0.82[AFR][1000 genomes]
rs7620228	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7627991	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs923470	0.82[AMR][1000 genomes]
rs923471	0.82[AMR][1000 genomes]
rs9289985	0.83[AMR][1000 genomes]
rs9810235	0.82[AMR][1000 genomes]
rs9823908	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9828079	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9833980	0.82[AMR][1000 genomes]
rs9837602	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9841186	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9851645	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9854260	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9860290	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9864437	0.82[AMR][1000 genomes]
rs9875878	0.83[AMR][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	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99795800-99866600	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99806200-99816000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:99806200-99818600	Weak transcription	HSMM	muscle
4	chr3:99809200-99815000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:99809200-99816800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:99809200-99823000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:99809200-99824400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:99809600-99815400	Weak transcription	Fetal Intestine Small	intestine
9	chr3:99809600-99815800	Weak transcription	Ovary	ovary
10	chr3:99809600-99817000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:99809600-99817200	Weak transcription	Small Intestine	intestine
12	chr3:99809600-99821200	Weak transcription	Aorta	Aorta
13	chr3:99809600-99822000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:99809800-99815800	Weak transcription	Psoas Muscle	Psoas
15	chr3:99809800-99815800	Weak transcription	HepG2	liver
16	chr3:99809800-99816200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:99809800-99816800	Weak transcription	Fetal Kidney	kidney
18	chr3:99809800-99816800	Weak transcription	Osteobl	bone
19	chr3:99809800-99818600	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:99809800-99822000	Weak transcription	Left Ventricle	heart
21	chr3:99809800-99822400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:99809800-99824400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:99811400-99817000	Weak transcription	Fetal Lung	lung
24	chr3:99812400-99816000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr3:99812600-99815800	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr3:99813000-99816800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:99813000-99817000	Weak transcription	NHDF-Ad	bronchial
28	chr3:99813000-99817000	Weak transcription	NHLF	lung
29	chr3:99813000-99823000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:99813000-99823600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:99813200-99815400	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr3:99813200-99816200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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