Variant report

Variant	rs13384787
Chromosome Location	chr2:231088084-231088085
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:231087067..231089892-chr2:231091301..231094794,3	K562	blood:
2	chr2:231088013..231089892-chr2:231091301..231094041,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10198539	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10201872	0.89[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10202244	0.89[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10209615	0.89[ASW][hapmap];0.94[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10498246	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13385151	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13397985	0.89[CEU][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13426106	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1946410	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28445040	0.89[CEU][hapmap];0.81[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28693552	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34855578	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35008063	0.88[EUR][1000 genomes]
rs35857956	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6436922	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6705808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6716753	0.84[CEU][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6738805	0.88[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs6743984	0.84[CEU][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs7423615	0.89[CEU][hapmap];0.80[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7557418	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7563433	0.88[CEU][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7584894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9989735	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9989746	1.00[CEU][hapmap];0.90[GIH][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9989835	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9989899	0.89[CEU][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv584666	chr2:231050715-231106621	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	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
rs13384787	SP110	Cis_1M	lymphoblastoid	RTeQTL
rs13384787	SP140	cis	multi-tissue	Pritchard
rs13384787	SP140	cis	lymphoblastoid	seeQTL
rs13384787	SP140	Cis_1M	lymphoblastoid	RTeQTL
rs13384787	SP110	cis	lymphoblastoid	seeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231085000-231094800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:231085200-231088400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:231085200-231089600	Enhancers	Primary B cells from peripheral blood	blood
4	chr2:231085400-231088200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:231085400-231088200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:231085400-231088400	Enhancers	Primary B cells from cord blood	blood
7	chr2:231085400-231088400	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr2:231085400-231088600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:231085400-231088600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr2:231085400-231088600	Weak transcription	Spleen	Spleen
11	chr2:231085400-231088800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr2:231085400-231088800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr2:231085400-231089000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:231085400-231089200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr2:231085400-231089400	Weak transcription	Primary T cells from cord blood	blood
16	chr2:231085400-231089400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr2:231085400-231089800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr2:231085400-231090000	Weak transcription	Esophagus	oesophagus
19	chr2:231085400-231090600	Weak transcription	Small Intestine	intestine
20	chr2:231085400-231092000	Weak transcription	Pancreas	Pancrea
21	chr2:231085600-231088400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr2:231085600-231088400	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr2:231085600-231088600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr2:231085600-231089000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:231085600-231089200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr2:231085600-231090200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:231086000-231088400	Enhancers	NHEK	skin
28	chr2:231086000-231088800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:231086400-231088200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:231086400-231088600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr2:231086400-231090400	Weak transcription	Fetal Thymus	thymus
32	chr2:231086400-231095000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:231086600-231088200	Enhancers	Placenta	Placenta
34	chr2:231086800-231088400	Enhancers	GM12878-XiMat	blood
35	chr2:231087400-231088600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:231087800-231088200	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr2:231087800-231089800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:231088000-231089200	Enhancers	Primary neutrophils fromperipheralblood	blood

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