Variant report

Variant	rs2223286
Chromosome Location	chr1:169665632-169665633
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12742961	0.85[JPT][hapmap]
rs12938	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs2272917	0.85[JPT][hapmap]
rs2272918	0.85[JPT][hapmap]
rs3917458	0.85[JPT][hapmap]
rs3917460	0.82[JPT][hapmap]
rs4140655	0.86[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs4987342	0.82[CHB][hapmap]
rs4987353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4987358	0.86[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs4987360	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4987367	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987369	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4987396	0.85[JPT][hapmap]
rs5355	0.85[JPT][hapmap]
rs6691453	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532586	chr1:169593222-169713184	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv872539	chr1:169658586-169674590	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1009313	chr1:169661299-169680173	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2223286	SELL	cis	lymphoblastoid	seeQTL
rs2223286	C1orf112,SCYL3	cis	brain	BrainEAC
rs2223286	C1orf112	cis	cerebellum	SCAN
rs2223286	SELL	cis	multi-tissue	Pritchard
rs2223286	BAT2L2	cis	cerebellum	SCAN
rs2223286	SCYL3	cis	parietal	SCAN
rs2223286	C1orf112	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169653200-169671600	Weak transcription	Spleen	Spleen
2	chr1:169658400-169666200	Enhancers	Thymus	Thymus
3	chr1:169662000-169665800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:169662000-169667400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:169662400-169676000	Genic enhancers	Primary B cells from peripheral blood	blood
6	chr1:169663200-169669000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:169663200-169674000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:169663800-169665800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
9	chr1:169664000-169666200	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
10	chr1:169664000-169666200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:169664000-169673400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:169664000-169674000	Genic enhancers	Fetal Thymus	thymus
13	chr1:169664000-169674200	Genic enhancers	Primary T cells fromperipheralblood	blood
14	chr1:169664200-169670400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr1:169664400-169665800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr1:169664400-169665800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:169664400-169665800	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:169664400-169670800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr1:169664600-169665800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
20	chr1:169664800-169665800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:169664800-169666200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:169664800-169669600	Genic enhancers	Dnd41	blood
23	chr1:169665000-169666400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr1:169665200-169666400	Enhancers	HUVEC	blood vessel
25	chr1:169665200-169667200	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr1:169665200-169668000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr1:169665400-169666200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells	blood
28	chr1:169665400-169666200	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr1:169665400-169666800	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
30	chr1:169665400-169669600	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr1:169665600-169665800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
32	chr1:169665600-169666000	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
33	chr1:169665600-169666000	Flanking Active TSS	GM12878-XiMat	blood

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