Variant report

Variant	rs28445040
Chromosome Location	chr2:231110582-231110583
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SP140-1	chr2:231110579-231110628	NONHSAT077272

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10198539	0.88[CEU][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10201872	0.89[CEU][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10202244	0.89[CEU][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10209615	0.83[CEU][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10498246	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12694867	1.00[CHD][hapmap]
rs13384787	0.89[CEU][hapmap];0.81[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13385151	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13397985	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13426106	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1946410	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28693552	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34855578	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35857956	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6436922	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6705808	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6710287	1.00[CHD][hapmap]
rs6710297	1.00[CHD][hapmap];0.88[GIH][hapmap]
rs6716753	0.94[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6743984	0.94[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs7423615	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7557418	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7563433	1.00[CEU][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7584894	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs890581	0.89[CEU][hapmap]
rs9989735	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9989746	0.89[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9989835	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9989899	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs28445040	SP140	cis	multi-tissue	Pritchard
rs28445040	SP140	cis	lymphoblastoid	seeQTL
rs28445040	TRIP12	cis	parietal	SCAN
rs28445040	SP140	Cis_1M	lymphoblastoid	RTeQTL
rs28445040	SP110	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231090200-231170000	Weak transcription	Spleen	Spleen
2	chr2:231092600-231118400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr2:231093200-231113000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr2:231099400-231118000	Weak transcription	Primary T cells from cord blood	blood
5	chr2:231100800-231114200	Strong transcription	GM12878-XiMat	blood
6	chr2:231101200-231114600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr2:231101200-231115000	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr2:231101800-231121600	Strong transcription	Primary B cells from peripheral blood	blood
9	chr2:231103200-231118200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:231103800-231118200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr2:231104000-231117000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:231105000-231112600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:231105200-231110600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr2:231107600-231117600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:231107600-231119600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:231109000-231117000	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr2:231109000-231118800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:231109200-231115000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr2:231109400-231116000	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr2:231109600-231114600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:231109600-231120800	Strong transcription	Primary B cells from cord blood	blood
22	chr2:231110200-231111800	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr2:231110200-231112000	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr2:231110400-231110800	Enhancers	Monocytes-CD14+_RO01746	blood

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