Variant report

Variant	rs28693552
Chromosome Location	chr2:231119914-231119915
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10198539	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10201872	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10202244	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10209615	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10498246	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13023767	0.81[AMR][1000 genomes]
rs13384787	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13385151	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13397985	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13426106	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1946410	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28445040	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34855578	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35857956	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6436922	0.94[EUR][1000 genomes]
rs6705808	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6716753	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6743984	0.95[EUR][1000 genomes]
rs7423615	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7557418	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7563433	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7584894	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9989735	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9989746	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9989835	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9989899	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv869834	chr2:231045013-231139827	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv998291	chr2:231045388-231136278	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28693552	SP140	Cis_1M	lymphoblastoid	RTeQTL
rs28693552	SP140	cis	multi-tissue	Pritchard
rs28693552	SP110	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231090200-231170000	Weak transcription	Spleen	Spleen
2	chr2:231101800-231121600	Strong transcription	Primary B cells from peripheral blood	blood
3	chr2:231109600-231120800	Strong transcription	Primary B cells from cord blood	blood
4	chr2:231116600-231120600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:231118200-231120400	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr2:231118200-231120400	Strong transcription	GM12878-XiMat	blood
7	chr2:231118200-231120600	Enhancers	Dnd41	blood
8	chr2:231118200-231120800	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr2:231118400-231120400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr2:231118800-231120000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr2:231118800-231120400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr2:231118800-231121600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:231119200-231120000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr2:231119200-231141200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr2:231119400-231120000	Enhancers	Primary T cells fromperipheralblood	blood
16	chr2:231119400-231120200	Enhancers	Fetal Thymus	thymus
17	chr2:231119600-231120000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
18	chr2:231119600-231120600	Enhancers	Primary T cells from cord blood	blood
19	chr2:231119800-231120400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:231119800-231120400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:231119800-231120600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr2:231119800-231120600	Enhancers	Primary T helper cells fromperipheralblood	blood

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