Variant report

Variant	rs12823926
Chromosome Location	chr12:104948566-104948567
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11112094	0.92[CEU][hapmap];0.95[TSI][hapmap]
rs11613208	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1553840	0.86[JPT][hapmap]
rs17035819	0.83[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1704904	0.86[JPT][hapmap]
rs1795871	0.96[CEU][hapmap]
rs34784608	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6539159	0.86[JPT][hapmap]
rs7968613	0.86[JPT][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
rs12823926	GOLGA2B	cis	parietal	SCAN
rs12823926	CCDC53	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104930200-104957600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:104939200-104951200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:104940600-104958000	Weak transcription	K562	blood
4	chr12:104941200-104949200	Weak transcription	Fetal Brain Female	brain
5	chr12:104941200-104951400	Weak transcription	Thymus	Thymus
6	chr12:104941400-104948800	Weak transcription	Fetal Thymus	thymus
7	chr12:104941400-104949400	Weak transcription	Lung	lung
8	chr12:104941400-104959400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:104942000-104957600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:104942800-104948800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:104944200-104948600	Weak transcription	HMEC	breast
12	chr12:104944200-104948800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:104944400-104957600	Weak transcription	A549	lung
14	chr12:104944600-104948800	Weak transcription	Small Intestine	intestine
15	chr12:104944600-104949200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr12:104944800-104951600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr12:104945800-104949200	Weak transcription	Brain Germinal Matrix	brain
18	chr12:104945800-104949400	Weak transcription	Fetal Brain Male	brain
19	chr12:104946000-104949400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:104946200-104949000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr12:104946400-104949000	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr12:104946600-104949400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:104946600-104950000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:104946600-104950200	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr12:104946800-104949400	Weak transcription	Right Ventricle	heart
26	chr12:104947200-104950800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:104947400-104958000	Weak transcription	Primary T cells from cord blood	blood
28	chr12:104947600-104949800	Enhancers	Primary T cells fromperipheralblood	blood
29	chr12:104947600-104952800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:104947800-104954600	Weak transcription	Primary B cells from cord blood	blood
31	chr12:104947800-104961200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr12:104947800-104964400	Weak transcription	Aorta	Aorta
33	chr12:104948000-104949400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr12:104948000-104949400	Weak transcription	Dnd41	blood
35	chr12:104948000-104949600	Enhancers	Primary B cells from peripheral blood	blood
36	chr12:104948000-104950000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:104948000-104950000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:104948000-104950000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr12:104948000-104950200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:104948000-104952600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr12:104948000-104954200	Weak transcription	GM12878-XiMat	blood
42	chr12:104948000-104957600	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr12:104948200-104948600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr12:104948200-104948800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr12:104948200-104948800	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr12:104948200-104949000	Enhancers	Placenta	Placenta
47	chr12:104948200-104950200	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr12:104948200-104951600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:104948200-104954800	Weak transcription	Spleen	Spleen
50	chr12:104948400-104948800	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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