Variant report

Variant	rs4237965
Chromosome Location	chr12:10396528-10396529
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10772249	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10772251	0.82[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10845084	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10845085	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10845086	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10845088	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10845089	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10845090	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10845091	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10845103	0.94[CEU][hapmap]
rs11053699	0.99[EUR][1000 genomes]
rs11053704	0.99[EUR][1000 genomes]
rs11053711	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11053712	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11613226	1.00[CEU][hapmap]
rs12370398	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs12372618	1.00[CEU][hapmap]
rs17808261	1.00[CEU][hapmap]
rs17808267	0.95[CEU][hapmap]
rs17808345	0.90[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2087308	1.00[JPT][hapmap]
rs2270238	0.80[TSI][hapmap]
rs3898120	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3898122	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4329754	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4763478	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55855636	0.99[EUR][1000 genomes]
rs56146423	0.99[EUR][1000 genomes]
rs56374289	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61919791	0.99[EUR][1000 genomes]
rs61919792	0.99[EUR][1000 genomes]
rs61919793	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7304038	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7309431	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7953558	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7970236	1.00[JPT][hapmap]
rs7978029	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1054811	chr12:10350587-10440005	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4237965	NOP2	cis	cerebellum	SCAN
rs4237965	PEX5	cis	parietal	SCAN
rs4237965	GRIN2B	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10376400-10397600	Weak transcription	Aorta	Aorta
2	chr12:10377200-10399000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr12:10377800-10404400	Weak transcription	Left Ventricle	heart
4	chr12:10387200-10396800	Weak transcription	Liver	Liver
5	chr12:10392600-10396600	Weak transcription	Adipose Nuclei	Adipose
6	chr12:10393400-10398200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:10394800-10397200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr12:10394800-10397200	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr12:10395000-10397200	Enhancers	Dnd41	blood
10	chr12:10395200-10397200	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr12:10395800-10402400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:10396000-10396800	Weak transcription	Placenta	Placenta
13	chr12:10396000-10397000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
14	chr12:10396200-10396600	Active TSS	HepG2	liver
15	chr12:10396200-10396800	Active TSS	Primary monocytes fromperipheralblood	blood
16	chr12:10396200-10396800	Enhancers	Primary T cells from cord blood	blood
17	chr12:10396200-10396800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:10396200-10397000	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr12:10396200-10397000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr12:10396200-10397000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr12:10396200-10397000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr12:10396200-10397000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:10396200-10397000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:10396200-10397000	Flanking Active TSS	GM12878-XiMat	blood
25	chr12:10396400-10396600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
26	chr12:10396400-10396600	Active TSS	Osteobl	bone
27	chr12:10396400-10396800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:10396400-10396800	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr12:10396400-10396800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr12:10396400-10396800	Flanking Active TSS	Fetal Thymus	thymus
31	chr12:10396400-10396800	Flanking Active TSS	Thymus	Thymus
32	chr12:10396400-10396800	Active TSS	Monocytes-CD14+_RO01746	blood
33	chr12:10396400-10397000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr12:10396400-10397000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:10396400-10397000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:10396400-10397000	Active TSS	K562	blood
37	chr12:10396400-10397200	Enhancers	Primary T helper cells fromperipheralblood	blood

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