Variant report

Variant	rs3372
Chromosome Location	chr11:65485218-65485219
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs10896027	0.83[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10896043	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs11227248	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11227249	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11227250	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11227261	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11227283	0.84[ASN][1000 genomes]
rs11227284	0.81[ASN][1000 genomes]
rs11227288	0.81[ASN][1000 genomes]
rs11227302	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs1151488	0.85[CHB][hapmap]
rs1193851	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs1205259	0.85[CHB][hapmap];0.89[CHD][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.87[ASN][1000 genomes]
rs12281400	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1784223	0.85[CHB][hapmap];0.85[CHD][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs1787034	0.85[CHB][hapmap];0.94[CHD][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs2448490	0.86[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2509948	1.00[MEX][hapmap];0.87[TSI][hapmap]
rs34007146	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34462081	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4930156	1.00[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4930304	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494003	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs535111	0.84[CEU][hapmap];0.86[YRI][hapmap]
rs573589	0.92[ASW][hapmap];0.84[CEU][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.86[YRI][hapmap]
rs578056	0.81[ASN][1000 genomes]
rs7122657	0.85[CHB][hapmap]
rs7395672	0.92[ASW][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap];0.86[YRI][hapmap]
rs7944860	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[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	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
2	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
3	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs3372	SNX32	cis	cerebellum	SCAN
rs3372	RNASEH2C	cis	Liver	GTEx
rs3372	ENSG00000172922	cis	multi-tissue	Pritchard
rs3372	MRPL11	cis	multi-tissue	Pritchard
rs3372	SNX32	cis	parietal	SCAN
rs3372	SIPA1	cis	cerebellum	SCAN
rs3372	RNASEH2C	cis	parietal	SCAN
rs3372	RNASEH2C	cis	multi-tissue	Pritchard
rs3372	RNASEH2C	cis	Artery Tibial	GTEx
rs3372	SNORA57	cis	parietal	SCAN
rs3372	SIPA1	cis	Liver	GTEx
rs3372	ZBTB3	cis	parietal	SCAN
rs3372	SLC22A10	cis	parietal	SCAN
rs3372	SIPA1	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65480000-65487400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:65480600-65485800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr11:65480600-65486400	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:65480600-65486600	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr11:65480600-65486800	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr11:65480600-65486800	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr11:65480800-65485400	Strong transcription	Psoas Muscle	Psoas
8	chr11:65480800-65485600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr11:65480800-65485600	Strong transcription	Liver	Liver
10	chr11:65480800-65485600	Strong transcription	Placenta Amnion	Placenta Amnion
11	chr11:65480800-65485600	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr11:65480800-65485800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr11:65480800-65485800	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr11:65480800-65486000	Strong transcription	Thymus	Thymus
15	chr11:65480800-65486200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr11:65480800-65486200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:65480800-65486200	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr11:65480800-65486200	Strong transcription	Lung	lung
19	chr11:65480800-65486200	Strong transcription	NHEK	skin
20	chr11:65480800-65486200	Strong transcription	NHLF	lung
21	chr11:65480800-65486400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:65480800-65486400	Strong transcription	Ovary	ovary
23	chr11:65480800-65486600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr11:65480800-65486600	Strong transcription	A549	lung
25	chr11:65480800-65486800	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr11:65480800-65486800	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr11:65480800-65486800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr11:65480800-65486800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr11:65480800-65486800	Strong transcription	Aorta	Aorta
30	chr11:65480800-65487000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:65481000-65485400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr11:65481000-65485400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr11:65481000-65485600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr11:65481000-65485600	Strong transcription	Colon Smooth Muscle	Colon
35	chr11:65481000-65485800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr11:65481000-65485800	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr11:65481000-65485800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr11:65481000-65485800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr11:65481000-65485800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr11:65481000-65485800	Strong transcription	Adipose Nuclei	Adipose
41	chr11:65481000-65485800	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr11:65481000-65485800	Strong transcription	Fetal Thymus	thymus
43	chr11:65481000-65485800	Strong transcription	Gastric	stomach
44	chr11:65481000-65485800	Strong transcription	HSMM	muscle
45	chr11:65481000-65485800	Strong transcription	NHDF-Ad	bronchial
46	chr11:65481000-65486000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr11:65481000-65486000	Strong transcription	Primary B cells from cord blood	blood
48	chr11:65481000-65486000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr11:65481000-65486000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr11:65481000-65486000	Strong transcription	K562	blood

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