Variant report

Variant	rs1553970
Chromosome Location	chr3:111323111-111323112
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11707702	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13078891	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13086157	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1398747	0.82[CEU][hapmap]
rs1606503	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2036995	0.92[ASW][hapmap];0.82[CEU][hapmap];0.82[CHB][hapmap];0.92[MEX][hapmap];0.81[AFR][1000 genomes]
rs2036996	0.81[CEU][hapmap]
rs4682052	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682292	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682295	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs867293	0.85[CEU][hapmap];0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv997756	chr3:111226058-111376585	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1553970	ZBED2	cis	lymphoblastoid	seeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111299400-111328600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr3:111314000-111326800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:111314200-111323400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:111314200-111327200	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr3:111314400-111324000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:111314400-111328600	Weak transcription	Thymus	Thymus
7	chr3:111315600-111323400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:111317800-111326000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr3:111318600-111326800	Strong transcription	Primary T cells from cord blood	blood
10	chr3:111318800-111323200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr3:111321000-111323200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:111321600-111325200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:111321600-111326200	Strong transcription	Fetal Thymus	thymus
14	chr3:111321600-111328200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
15	chr3:111322000-111323200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
16	chr3:111322000-111324000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:111322200-111323600	Enhancers	Primary B cells from cord blood	blood
18	chr3:111322200-111323600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:111322200-111323800	Enhancers	Primary B cells from peripheral blood	blood
20	chr3:111322400-111325200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr3:111322600-111323400	Genic enhancers	Dnd41	blood
22	chr3:111322600-111324400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:111322600-111326600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:111322800-111323200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:111322800-111323200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:111322800-111324800	Enhancers	Osteobl	bone
27	chr3:111323000-111323200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:111323000-111323200	Enhancers	Esophagus	oesophagus
29	chr3:111323000-111323400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr3:111323000-111324200	Enhancers	NHEK	skin
31	chr3:111323000-111324400	Enhancers	Muscle Satellite Cultured Cells	--

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