Variant report

Variant	rs7558428
Chromosome Location	chr2:182018554-182018555
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10171108	1.00[JPT][hapmap]
rs10171998	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10187842	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10930950	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11684463	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11688120	0.98[ASN][1000 genomes]
rs11692625	0.98[ASN][1000 genomes]
rs11891215	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11893772	0.94[ASN][1000 genomes]
rs11893821	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621277	1.00[JPT][hapmap]
rs12989967	1.00[JPT][hapmap]
rs12999974	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13004683	0.84[ASN][1000 genomes]
rs13004750	0.86[ASN][1000 genomes]
rs13011738	0.98[ASN][1000 genomes]
rs13019038	0.82[ASN][1000 genomes]
rs13020845	1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap]
rs13025711	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13026070	0.92[ASN][1000 genomes]
rs13029368	1.00[JPT][hapmap]
rs13031518	0.94[ASN][1000 genomes]
rs13033467	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34366526	0.84[AMR][1000 genomes]
rs34467063	0.98[ASN][1000 genomes]
rs34504038	0.98[ASN][1000 genomes]
rs34601234	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34714467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34825850	0.94[ASN][1000 genomes]
rs35049898	0.89[EUR][1000 genomes]
rs35076700	0.98[ASN][1000 genomes]
rs35323141	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35482602	0.98[ASN][1000 genomes]
rs35543145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35702511	0.98[ASN][1000 genomes]
rs35725888	0.94[ASN][1000 genomes]
rs4346343	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4366861	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4432412	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4510177	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs4595925	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4667008	0.86[JPT][hapmap]
rs4990275	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs55664819	0.88[EUR][1000 genomes]
rs55900432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55954384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56169464	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59395276	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59639779	0.88[ASN][1000 genomes]
rs62178846	0.88[EUR][1000 genomes]
rs6433878	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6433879	0.82[CHB][hapmap]
rs6433883	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6433892	0.95[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs6433895	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6704750	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6706397	0.91[CEU][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs6706696	0.89[EUR][1000 genomes]
rs6710650	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs6711938	0.89[EUR][1000 genomes]
rs6713632	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6731268	1.00[JPT][hapmap]
rs6743720	0.90[ASN][1000 genomes]
rs6744130	0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6745190	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6746347	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759865	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72887083	0.98[ASN][1000 genomes]
rs7349232	0.86[ASN][1000 genomes]
rs7371639	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7559803	1.00[JPT][hapmap]
rs7566146	0.89[EUR][1000 genomes]
rs7566256	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7566434	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7569991	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs7580796	0.89[EUR][1000 genomes]
rs7581267	0.92[ASN][1000 genomes]
rs7592486	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7598960	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808318	0.82[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431824	chr2:181946115-182118559	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv459954	chr2:181975252-182040293	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv583910	chr2:181975252-182040293	ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:181999600-182022000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:182010800-182021000	Weak transcription	Fetal Thymus	thymus
3	chr2:182011400-182020800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:182014400-182027600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:182015800-182019200	Enhancers	Primary T cells from cord blood	blood
6	chr2:182016200-182018600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr2:182016200-182018600	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr2:182016200-182019000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr2:182016600-182018600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:182016600-182018800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:182016600-182019000	Enhancers	Dnd41	blood
12	chr2:182016600-182019200	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr2:182016600-182019200	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr2:182016800-182019400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:182017000-182019000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:182017800-182020800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr2:182017800-182020800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr2:182018200-182019000	Weak transcription	Fetal Lung	lung
19	chr2:182018200-182019000	Enhancers	Fetal Stomach	stomach
20	chr2:182018400-182018600	Enhancers	Primary T helper naive cells from peripheral blood	blood

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