Variant report

Variant	rs10861233
Chromosome Location	chr12:104958306-104958307
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10861232	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1344676	1.00[LWK][hapmap]
rs1650128	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1810133	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4964821	0.83[CEU][hapmap]

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	nsv832504	chr12:104853331-105028245	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1035364	chr12:104948307-105003705	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10861233	GNN	cis	cerebellum	SCAN
rs10861233	NUAK1	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104941400-104959400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr12:104947800-104961200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr12:104947800-104964400	Weak transcription	Aorta	Aorta
4	chr12:104949000-104959400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:104949000-104960400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr12:104949000-104961400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr12:104949600-104968800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:104949800-104963400	Weak transcription	Lung	lung
9	chr12:104950000-104978800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:104950200-104959200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:104951600-104959400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:104951600-104959600	Weak transcription	Brain Anterior Caudate	brain
13	chr12:104951600-104962200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr12:104955200-104961800	Weak transcription	Spleen	Spleen
15	chr12:104955600-104962000	Weak transcription	Gastric	stomach
16	chr12:104956200-104959600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:104957000-104959000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
18	chr12:104957000-104959000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
19	chr12:104957000-104959000	ZNF genes & repeats	GM12878-XiMat	blood
20	chr12:104957200-104958600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:104957200-104958800	ZNF genes & repeats	Primary B cells from cord blood	blood
22	chr12:104957200-104958800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
23	chr12:104957200-104962400	Genic enhancers	Dnd41	blood
24	chr12:104957400-104958800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:104957400-104959000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr12:104957600-104958400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:104957600-104958400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
28	chr12:104957600-104958400	ZNF genes & repeats	Fetal Thymus	thymus
29	chr12:104957600-104958400	ZNF genes & repeats	Thymus	Thymus
30	chr12:104957600-104958400	Strong transcription	A549	lung
31	chr12:104957600-104958600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:104957600-104958600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:104957600-104958800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:104957600-104958800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr12:104957600-104959000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
36	chr12:104957600-104959000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:104957800-104958400	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr12:104957800-104958400	ZNF genes & repeats	Fetal Brain Female	brain
39	chr12:104957800-104958800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
40	chr12:104958000-104958400	ZNF genes & repeats	Primary T cells from cord blood	blood
41	chr12:104958000-104958400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:104958000-104958600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
43	chr12:104958000-104959000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr12:104958000-104959600	Weak transcription	Brain Substantia Nigra	brain
45	chr12:104958200-104958400	Strong transcription	K562	blood

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