Variant report

Variant	rs16839882
Chromosome Location	chr3:98232901-98232902
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:98231079..98233365-chr3:98241378..98242915,2	MCF-7	breast:
2	chr3:98228978..98234732-chr3:98235993..98241855,11	K562	blood:
3	chr3:98226040..98228792-chr3:98229114..98233536,5	K562	blood:
4	chr3:98230310..98236256-chr3:98236426..98241825,8	K562	blood:
5	chr3:98200387..98203207-chr3:98231442..98233594,2	MCF-7	breast:
6	chr3:98223162..98227704-chr3:98229534..98233536,4	K562	blood:

Variant related genes	Relation type
ENSG00000080822	Chromatin interaction
ENSG00000248839	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1471299	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16839839	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16846235	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1961152	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56787128	1.00[EUR][1000 genomes]
rs57985907	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58755405	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58756404	1.00[EUR][1000 genomes]
rs59248577	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60788607	1.00[EUR][1000 genomes]
rs61642998	1.00[EUR][1000 genomes]
rs7626745	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[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	nsv528056	chr3:98101101-98317836	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv520503	chr3:98102801-98317836	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv834774	chr3:98108423-98274064	Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv834775	chr3:98170059-98367552	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98206800-98240800	Weak transcription	Pancreas	Pancrea
2	chr3:98216800-98235400	Weak transcription	Left Ventricle	heart
3	chr3:98219200-98233200	Weak transcription	Psoas Muscle	Psoas
4	chr3:98220400-98235400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr3:98220400-98235400	Weak transcription	Gastric	stomach
6	chr3:98220400-98235400	Weak transcription	Spleen	Spleen
7	chr3:98220800-98233400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr3:98221000-98238200	Weak transcription	Small Intestine	intestine
9	chr3:98222600-98233000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:98223600-98233600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:98223800-98233800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:98223800-98234200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:98223800-98235400	Weak transcription	Ovary	ovary
14	chr3:98223800-98235600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:98224000-98233200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr3:98224000-98235400	Weak transcription	Lung	lung
17	chr3:98224000-98235600	Weak transcription	Fetal Lung	lung
18	chr3:98224000-98235600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:98225000-98240800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:98225600-98233800	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr3:98225600-98233800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr3:98225600-98235400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:98226200-98234200	Weak transcription	Liver	Liver
24	chr3:98226600-98237800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:98227000-98233600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr3:98227200-98233800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:98227200-98234200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:98228000-98240000	Weak transcription	Right Ventricle	heart
29	chr3:98228000-98240000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:98228200-98234200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:98228200-98234200	Weak transcription	Fetal Intestine Large	intestine
32	chr3:98228200-98234600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:98228400-98240000	Weak transcription	Fetal Kidney	kidney
34	chr3:98228600-98233800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:98228600-98234400	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:98228600-98240200	Weak transcription	Colonic Mucosa	Colon
37	chr3:98229000-98233000	Strong transcription	Primary T cells from cord blood	blood
38	chr3:98229000-98234400	Weak transcription	Fetal Brain Female	brain
39	chr3:98229000-98234800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr3:98229000-98235600	Weak transcription	Aorta	Aorta
41	chr3:98229000-98237200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr3:98229200-98234200	Weak transcription	Dnd41	blood
43	chr3:98229200-98237800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr3:98229200-98238200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr3:98229200-98239200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:98229400-98233800	Weak transcription	GM12878-XiMat	blood
47	chr3:98229600-98235000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr3:98229600-98235400	Weak transcription	Esophagus	oesophagus
49	chr3:98229800-98237200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:98230000-98233200	Enhancers	Brain Inferior Temporal Lobe	brain

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