Variant report

Variant	rs16858238
Chromosome Location	chr3:111259277-111259278
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11928364	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11928649	1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16858215	0.94[AFR][1000 genomes]
rs16858218	0.82[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16858221	0.85[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16858237	0.82[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16858274	0.85[JPT][hapmap];0.87[AMR][1000 genomes]
rs16858276	0.87[AMR][1000 genomes]
rs16858277	0.85[JPT][hapmap];0.87[AMR][1000 genomes]
rs16858280	0.85[JPT][hapmap];0.87[AMR][1000 genomes]
rs16858281	0.87[AMR][1000 genomes]
rs2276872	0.85[JPT][hapmap];0.87[AMR][1000 genomes]
rs57476687	0.87[AMR][1000 genomes]
rs57590158	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58906230	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60925257	0.87[AMR][1000 genomes]
rs60973340	0.87[AMR][1000 genomes]
rs721335	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72622318	0.87[AMR][1000 genomes]
rs72622319	0.87[AMR][1000 genomes]
rs72622320	0.87[AMR][1000 genomes]
rs72622321	0.87[AMR][1000 genomes]
rs73852803	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73855136	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73855137	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73855138	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73855139	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73855140	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73855144	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73855145	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7629206	0.85[JPT][hapmap];0.87[AMR][1000 genomes]
rs981953	0.82[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs981954	0.85[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs981955	0.85[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv997756	chr3:111226058-111376585	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv3946	chr3:111236035-111283038	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111255800-111264400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:111257200-111261000	Enhancers	Primary B cells from peripheral blood	blood
3	chr3:111257800-111259400	Flanking Active TSS	Primary T cells from cord blood	blood
4	chr3:111258000-111260200	Weak transcription	Small Intestine	intestine
5	chr3:111258000-111261200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:111258600-111260000	Weak transcription	NH-A	brain
7	chr3:111258600-111260600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr3:111258600-111260600	Enhancers	Fetal Thymus	thymus
9	chr3:111258600-111260800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:111258600-111265200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:111258600-111266800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:111258800-111259400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:111258800-111259600	Enhancers	Thymus	Thymus
14	chr3:111258800-111259800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:111258800-111260000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:111258800-111260000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:111258800-111260200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:111258800-111260200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr3:111258800-111260200	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr3:111258800-111260200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:111258800-111260400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:111258800-111260400	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr3:111258800-111260400	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr3:111258800-111260400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:111258800-111260400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr3:111258800-111260400	Weak transcription	Fetal Lung	lung
27	chr3:111258800-111260800	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr3:111258800-111260800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:111258800-111261000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr3:111258800-111264200	Weak transcription	Stomach Mucosa	stomach
31	chr3:111258800-111266600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:111259000-111259600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr3:111259000-111260000	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr3:111259000-111260200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:111259000-111260200	Enhancers	Dnd41	blood
36	chr3:111259000-111260800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr3:111259000-111264000	Weak transcription	Fetal Intestine Small	intestine
38	chr3:111259200-111260200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr3:111259200-111260600	Weak transcription	Primary B cells from cord blood	blood

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