Variant report

Variant	rs16988291
Chromosome Location	chr22:30501105-30501106
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30500122..30506829-chr22:30640771..30648697,14	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LIF-3	chr22:30501083-30501397	NONHSAT084758

Variant related genes	Relation type
ENSG00000128342	Chromatin interaction
ENSG00000268812	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs11552852	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1544429	0.89[EUR][1000 genomes]
rs1544430	0.81[EUR][1000 genomes]
rs1544431	0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1544433	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16988120	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16988143	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16988148	0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16988149	0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16988244	1.00[CEU][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16988303	1.00[CEU][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16988304	1.00[CEU][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16988333	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17647863	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17648208	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1807726	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2412980	1.00[CEU][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2412981	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36579	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36588	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36589	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36592	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36593	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36597	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs36599	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36602	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36603	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36608	0.84[EUR][1000 genomes]
rs39713	0.85[EUR][1000 genomes]
rs41278853	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41281623	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41281633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4482600	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4482601	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs45629133	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4823078	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55645000	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56392746	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56406718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57348516	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5752977	0.82[EUR][1000 genomes]
rs5752979	0.89[EUR][1000 genomes]
rs5753038	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5753039	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5753042	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5753043	1.00[CEU][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5763582	0.80[EUR][1000 genomes]
rs5763595	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5763855	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5763856	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5763857	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5763858	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5763870	1.00[CEU][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5763873	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5763878	1.00[CEU][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58162368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6006383	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60759987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6518681	0.91[EUR][1000 genomes]
rs6519802	0.92[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6519805	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs713916	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7284365	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7284951	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7285585	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7286205	1.00[CEU][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7286441	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7287233	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7290175	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs737901	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs737938	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73883344	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73883349	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs73883354	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73883355	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73883359	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73883360	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73883363	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73883367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73883370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73883374	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73883375	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73883377	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73883378	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8141471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs962322	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv588884	chr22:30494371-30590026	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30499400-30501800	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr22:30499400-30502000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr22:30499800-30501400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr22:30499800-30501600	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr22:30499800-30501800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr22:30499800-30502000	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr22:30500000-30501800	Enhancers	Primary T cells from cord blood	blood
8	chr22:30500000-30501800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr22:30500000-30502000	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr22:30500200-30501200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr22:30500200-30501200	Enhancers	NH-A	brain
12	chr22:30500200-30501400	Enhancers	Primary hematopoietic stem cells	blood
13	chr22:30500200-30501400	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr22:30500200-30501600	Enhancers	HSMM	muscle
15	chr22:30500200-30501800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr22:30500400-30501200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr22:30500400-30501200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr22:30500400-30501400	Enhancers	Fetal Thymus	thymus
19	chr22:30500400-30501800	Enhancers	Osteobl	bone
20	chr22:30500400-30502000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr22:30500600-30501400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr22:30500600-30501800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr22:30500800-30501200	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr22:30500800-30501800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr22:30501000-30501400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr22:30501000-30501400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr22:30501000-30501400	Enhancers	Primary T cells fromperipheralblood	blood
28	chr22:30501000-30501400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr22:30501000-30501400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr22:30501000-30501600	Enhancers	Thymus	Thymus
31	chr22:30501000-30502000	Flanking Active TSS	Dnd41	blood

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