Variant report

Variant	rs11128125
Chromosome Location	chr3:69389614-69389615
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1564758	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1976064	0.88[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2003264	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2005546	0.89[CEU][hapmap];0.80[CHB][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2008239	1.00[ASW][hapmap];0.89[CEU][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34397489	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6549200	0.88[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6549204	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6763080	0.93[ASN][1000 genomes]
rs6774290	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs6781841	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6802833	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6808107	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7610748	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7615137	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7640281	0.96[ASN][1000 genomes]
rs9820308	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.84[LWK][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9820322	0.99[ASN][1000 genomes]
rs9867072	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9869925	0.80[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9872564	0.80[CHB][hapmap]
rs9876410	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.87[YRI][hapmap];0.93[ASN][1000 genomes]
rs9882259	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv876935	chr3:69307942-69401248	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1007730	chr3:69355932-69730587	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv1800315	chr3:69374729-69414587	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11128125	S100A12	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69372200-69403800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:69378400-69390600	Weak transcription	Thymus	Thymus
3	chr3:69378400-69400600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:69380600-69393200	Weak transcription	HSMM	muscle
5	chr3:69380800-69390600	Weak transcription	Fetal Lung	lung
6	chr3:69384400-69389800	Weak transcription	Brain Anterior Caudate	brain
7	chr3:69384400-69390600	Weak transcription	Fetal Heart	heart
8	chr3:69384400-69390800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:69386000-69400200	Weak transcription	NHEK	skin
10	chr3:69387800-69389800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:69387800-69393600	Enhancers	Brain Hippocampus Middle	brain
12	chr3:69388000-69389800	Enhancers	Primary hematopoietic stem cells	blood
13	chr3:69388000-69390000	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr3:69388200-69391800	Enhancers	Brain Substantia Nigra	brain
15	chr3:69388400-69389800	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr3:69388600-69389800	Genic enhancers	HUVEC	blood vessel
17	chr3:69388600-69391000	Enhancers	Spleen	Spleen
18	chr3:69389000-69389800	Genic enhancers	Dnd41	blood
19	chr3:69389000-69390000	Enhancers	H9 Cell Line	embryonic stem cell
20	chr3:69389000-69390000	Enhancers	Brain Angular Gyrus	brain
21	chr3:69389000-69391800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:69389000-69400800	Weak transcription	Aorta	Aorta
23	chr3:69389200-69390400	Weak transcription	Right Atrium	heart
24	chr3:69389200-69390600	Weak transcription	Fetal Stomach	stomach
25	chr3:69389200-69392200	Weak transcription	Left Ventricle	heart
26	chr3:69389400-69390400	Weak transcription	Fetal Thymus	thymus
27	chr3:69389400-69391200	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr3:69389400-69400600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:69389600-69389800	Enhancers	Lung	lung
30	chr3:69389600-69390400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr3:69389600-69391400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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