Variant report

Variant	rs16858218
Chromosome Location	chr3:111257138-111257139
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11928364	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11928649	0.85[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16858221	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16858229	0.94[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs16858237	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16858238	0.82[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16858274	0.84[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes]
rs16858276	0.91[AMR][1000 genomes]
rs16858277	0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes]
rs16858280	1.00[TSI][hapmap];0.91[AMR][1000 genomes]
rs16858281	0.91[AMR][1000 genomes]
rs2276872	0.84[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes]
rs57476687	0.91[AMR][1000 genomes]
rs57590158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58085859	0.95[AFR][1000 genomes]
rs58195592	0.95[AFR][1000 genomes]
rs58906230	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60925257	0.91[AMR][1000 genomes]
rs60973340	0.91[AMR][1000 genomes]
rs721335	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72622318	0.91[AMR][1000 genomes]
rs72622319	0.91[AMR][1000 genomes]
rs72622320	0.91[AMR][1000 genomes]
rs72622321	0.91[AMR][1000 genomes]
rs72939542	0.90[AFR][1000 genomes]
rs73852803	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73855128	0.95[AFR][1000 genomes]
rs73855135	0.97[AFR][1000 genomes]
rs73855136	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73855137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73855138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73855139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73855140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73855144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73855145	0.96[AMR][1000 genomes]
rs7629206	1.00[TSI][hapmap];0.91[AMR][1000 genomes]
rs981953	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs981954	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs981955	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111253600-111257400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:111253800-111257200	Weak transcription	Hela-S3	cervix
3	chr3:111253800-111257200	Weak transcription	HMEC	breast
4	chr3:111253800-111257200	Weak transcription	NH-A	brain
5	chr3:111254200-111257200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:111254200-111257200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:111254200-111257200	Weak transcription	HSMM	muscle
8	chr3:111254200-111257200	Weak transcription	Osteobl	bone
9	chr3:111254200-111257400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:111254200-111257400	Weak transcription	HSMMtube	muscle
11	chr3:111254200-111257800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:111254400-111257200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:111254400-111257200	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr3:111254400-111257200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:111254400-111257400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:111254600-111257200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr3:111254600-111257200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr3:111254800-111257600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:111255200-111258000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:111255800-111264400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:111256000-111257200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr3:111256200-111257200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:111256200-111257600	Weak transcription	Small Intestine	intestine
24	chr3:111256400-111257200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr3:111256400-111257400	Weak transcription	Stomach Mucosa	stomach
26	chr3:111257000-111257200	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr3:111257000-111257200	Enhancers	Muscle Satellite Cultured Cells	--
28	chr3:111257000-111257400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:111257000-111257400	Enhancers	Dnd41	blood
30	chr3:111257000-111257600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:111257000-111257800	Enhancers	Primary T cells from cord blood	blood
32	chr3:111257000-111258400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:111257000-111258400	Enhancers	Primary T helper cells fromperipheralblood	blood

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