Variant report

Variant	rs2354531
Chromosome Location	chr5:49931637-49931638
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11950506	0.81[AMR][1000 genomes]
rs11952107	0.81[AMR][1000 genomes]
rs11954064	0.86[AMR][1000 genomes]
rs11955651	0.81[AMR][1000 genomes]
rs11955934	0.81[AMR][1000 genomes]
rs11959326	0.81[AMR][1000 genomes]
rs13153852	0.82[EUR][1000 genomes]
rs13156735	0.81[AMR][1000 genomes]
rs13157079	0.81[AMR][1000 genomes]
rs13157952	1.00[EUR][1000 genomes]
rs13159239	0.81[AMR][1000 genomes]
rs13159553	0.93[EUR][1000 genomes]
rs13162663	0.98[EUR][1000 genomes]
rs13163802	0.81[AMR][1000 genomes]
rs13167408	0.93[EUR][1000 genomes]
rs13169200	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13171248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13172426	0.84[EUR][1000 genomes]
rs13172836	0.93[EUR][1000 genomes]
rs13174498	0.81[AMR][1000 genomes]
rs13180485	0.82[EUR][1000 genomes]
rs13180506	0.93[EUR][1000 genomes]
rs13181117	0.81[AMR][1000 genomes]
rs13183686	0.93[EUR][1000 genomes]
rs13183910	0.81[AMR][1000 genomes]
rs13186653	0.81[AMR][1000 genomes]
rs13190144	0.81[AMR][1000 genomes]
rs1968637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34264957	0.81[AMR][1000 genomes]
rs34414061	0.81[AMR][1000 genomes]
rs34443769	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34677483	0.81[AMR][1000 genomes]
rs34827507	0.81[AMR][1000 genomes]
rs35128589	0.81[AMR][1000 genomes]
rs35210389	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35292338	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35347195	0.81[AMR][1000 genomes]
rs35434227	0.93[EUR][1000 genomes]
rs35473824	0.81[AMR][1000 genomes]
rs35596019	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36187734	0.93[EUR][1000 genomes]
rs41270305	0.81[AMR][1000 genomes]
rs6859621	0.81[AMR][1000 genomes]
rs6880398	0.81[AMR][1000 genomes]
rs6883701	0.81[AMR][1000 genomes]
rs6888271	0.81[AMR][1000 genomes]
rs6888315	0.81[AMR][1000 genomes]
rs6892149	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71615974	0.93[EUR][1000 genomes]
rs71615975	0.91[EUR][1000 genomes]
rs71615978	0.81[AMR][1000 genomes]
rs71615984	0.81[AMR][1000 genomes]
rs71631479	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71631481	0.84[EUR][1000 genomes]
rs7717073	0.81[AMR][1000 genomes]
rs7723395	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7726225	0.81[AMR][1000 genomes]
rs7730188	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7733931	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv2757995	chr5:49748352-50058182	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv2759342	chr5:49748352-50058182	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv964850	chr5:49883635-49942856	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv16870	chr5:49885849-49989415	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv14399	chr5:49885912-49934455	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv969047	chr5:49918610-49934158	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer	TF binding region	1 gene(s)	inside rSNPs	diseases
14	nsv969048	chr5:49931153-49934158	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2354531	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49926400-49934200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr5:49926600-49934200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr5:49926800-49934000	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr5:49926800-49934400	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr5:49927400-49932400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr5:49927400-49932800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr5:49928200-49931800	Enhancers	Primary T cells fromperipheralblood	blood
8	chr5:49928400-49932400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr5:49929000-49932400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr5:49929200-49932400	Enhancers	Fetal Thymus	thymus
11	chr5:49929400-49936200	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr5:49930000-49932400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:49930800-49931800	Enhancers	Dnd41	blood
14	chr5:49930800-49933400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr5:49931000-49932200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr5:49931000-49934200	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr5:49931000-49934800	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr5:49931400-49934000	Enhancers	Primary T cells from cord blood	blood
19	chr5:49931600-49932000	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr5:49931600-49932800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr5:49931600-49933400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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