Variant report

Variant	rs2399460
Chromosome Location	chr3:112771505-112771506
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112770714..112773506-chr3:112929174..112932492,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144857	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10460813	0.93[MEX][hapmap]
rs1110819	0.82[CHB][hapmap]
rs11718449	0.82[CEU][hapmap]
rs12495569	0.84[EUR][1000 genomes]
rs1809629	0.84[CHB][hapmap]
rs2276769	0.83[CHB][hapmap];0.93[MEX][hapmap]
rs34671634	0.83[EUR][1000 genomes]
rs3868879	0.82[CEU][hapmap];0.95[CHB][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3872609	0.81[CHB][hapmap]
rs6438125	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7642680	0.82[CEU][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7650483	0.84[ASW][hapmap];0.86[CHB][hapmap];0.87[MEX][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7650656	0.82[CEU][hapmap]
rs984706	0.82[CHB][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
rs2399460	GTPBP8	Cis_1M	lymphoblastoid	RTeQTL
rs2399460	C3orf17	cis	cerebellum	SCAN
rs2399460	SIDT1	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112763000-112789200	Weak transcription	HSMMtube	muscle
2	chr3:112770200-112771600	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr3:112770200-112771800	Enhancers	Rectal Smooth Muscle	rectum
4	chr3:112770200-112772200	Enhancers	Primary T cells from cord blood	blood
5	chr3:112770200-112776800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr3:112770200-112784400	Weak transcription	Primary B cells from cord blood	blood
7	chr3:112770400-112772000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr3:112770600-112771600	Enhancers	Colon Smooth Muscle	Colon
9	chr3:112770600-112771600	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr3:112770600-112771600	Enhancers	Stomach Smooth Muscle	stomach
11	chr3:112770600-112772400	Weak transcription	A549	lung
12	chr3:112770600-112773200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:112770600-112773200	Weak transcription	Liver	Liver
14	chr3:112770600-112773200	Weak transcription	HSMM	muscle
15	chr3:112770600-112773400	Weak transcription	Fetal Heart	heart
16	chr3:112770600-112774800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr3:112770600-112775600	Weak transcription	Brain Germinal Matrix	brain
18	chr3:112770600-112775800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:112770600-112780600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:112770600-112780800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:112770600-112781000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:112770600-112781800	Weak transcription	Left Ventricle	heart
23	chr3:112770600-112782000	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr3:112770600-112783800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:112770600-112784200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr3:112770600-112784400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr3:112770800-112771600	Weak transcription	Fetal Brain Female	brain
28	chr3:112770800-112773000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:112770800-112773600	Weak transcription	NH-A	brain
30	chr3:112770800-112773800	Enhancers	Fetal Brain Male	brain
31	chr3:112770800-112775000	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr3:112770800-112775800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:112770800-112781400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr3:112770800-112782200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr3:112770800-112783200	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:112770800-112787400	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr3:112771000-112771600	Enhancers	Brain Anterior Caudate	brain
38	chr3:112771000-112771600	Weak transcription	Ovary	ovary
39	chr3:112771000-112772200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:112771000-112773000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:112771000-112773000	Weak transcription	Osteobl	bone
42	chr3:112771000-112773200	Weak transcription	NHDF-Ad	bronchial
43	chr3:112771000-112773200	Weak transcription	NHEK	skin
44	chr3:112771000-112773400	Weak transcription	NHLF	lung
45	chr3:112771000-112774800	Weak transcription	GM12878-XiMat	blood
46	chr3:112771000-112775000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:112771000-112775400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:112771000-112777200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:112771000-112783800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr3:112771000-112784200	Weak transcription	Fetal Muscle Trunk	muscle

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