Variant report

Variant	rs12495569
Chromosome Location	chr3:112773601-112773602
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10460813	0.81[MEX][hapmap]
rs10934211	0.83[MEX][hapmap]
rs11718449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1488189	0.83[MEX][hapmap]
rs2276769	0.81[MEX][hapmap]
rs2399460	0.82[CEU][hapmap];0.87[MEX][hapmap];0.84[EUR][1000 genomes]
rs34671634	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3868879	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3872611	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3901416	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6438125	0.97[EUR][1000 genomes]
rs7620940	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7642680	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7650483	0.91[CEU][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs7650656	1.00[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs9288967	0.83[MEX][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv3951	chr3:112759554-112800236	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12495569	C3orf17	cis	cerebellum	SCAN
rs12495569	SIDT1	cis	cerebellum	SCAN
rs12495569	GTPBP8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112763000-112789200	Weak transcription	HSMMtube	muscle
2	chr3:112770200-112776800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr3:112770200-112784400	Weak transcription	Primary B cells from cord blood	blood
4	chr3:112770600-112774800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr3:112770600-112775600	Weak transcription	Brain Germinal Matrix	brain
6	chr3:112770600-112775800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:112770600-112780600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:112770600-112780800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:112770600-112781000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:112770600-112781800	Weak transcription	Left Ventricle	heart
11	chr3:112770600-112782000	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr3:112770600-112783800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:112770600-112784200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:112770600-112784400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:112770800-112773800	Enhancers	Fetal Brain Male	brain
16	chr3:112770800-112775000	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr3:112770800-112775800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:112770800-112781400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr3:112770800-112782200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:112770800-112783200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr3:112770800-112787400	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr3:112771000-112774800	Weak transcription	GM12878-XiMat	blood
23	chr3:112771000-112775000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:112771000-112775400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:112771000-112777200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:112771000-112783800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:112771000-112784200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr3:112771000-112798600	Weak transcription	Psoas Muscle	Psoas
29	chr3:112771200-112775800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:112771200-112788800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:112771400-112774800	Weak transcription	Fetal Lung	lung
32	chr3:112771400-112775400	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:112771400-112781800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:112771400-112782600	Weak transcription	Fetal Stomach	stomach
35	chr3:112771600-112775800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr3:112771600-112782600	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:112771600-112783800	Weak transcription	Brain Anterior Caudate	brain
38	chr3:112771800-112781600	Weak transcription	Ovary	ovary
39	chr3:112772000-112774600	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr3:112772000-112774800	Weak transcription	Fetal Brain Female	brain
41	chr3:112772200-112779200	Weak transcription	Primary T cells from cord blood	blood
42	chr3:112773000-112774000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:112773000-112774200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:112773000-112774200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:112773000-112774200	Enhancers	Osteobl	bone
46	chr3:112773000-112774400	Enhancers	HMEC	breast
47	chr3:112773000-112774600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:112773000-112774600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:112773200-112773800	Enhancers	Liver	Liver
50	chr3:112773200-112773800	Enhancers	HSMM	muscle

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