Variant report

Variant	rs13069904
Chromosome Location	chr3:140956600-140956601
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:140948502..140951500-chr3:140954182..140956854,2	MCF-7	breast:
2	chr3:140954329..140957093-chr3:140957221..140960303,3	K562	blood:

Variant related genes	Relation type
ENSG00000155893	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1026716	0.92[MEX][hapmap];0.91[TSI][hapmap]
rs10935425	0.86[TSI][hapmap]
rs10935427	0.89[TSI][hapmap]
rs12486843	0.86[EUR][1000 genomes]
rs13065438	0.85[EUR][1000 genomes]
rs1511371	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1511372	0.96[CEU][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs1511373	0.85[EUR][1000 genomes]
rs1877222	0.86[EUR][1000 genomes]
rs2048459	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2137016	0.82[TSI][hapmap]
rs2291039	0.93[EUR][1000 genomes]
rs2311733	0.84[MEX][hapmap]
rs4683585	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4683586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6779870	0.92[CEU][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs7613113	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7652530	0.96[CEU][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs9875630	0.93[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	nsv460870	chr3:140938546-141005574	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv591892	chr3:140938546-141005574	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13069904	ACPL2	cis	multi-tissue	Pritchard
rs13069904	ACPL2	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140951600-140956600	Weak transcription	Gastric	stomach
2	chr3:140951600-140957000	Weak transcription	Aorta	Aorta
3	chr3:140951600-140959000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:140951600-140979000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:140951800-140956600	Weak transcription	Fetal Lung	lung
6	chr3:140951800-140956800	Weak transcription	Right Atrium	heart
7	chr3:140951800-140956800	Weak transcription	Stomach Mucosa	stomach
8	chr3:140951800-140958800	Weak transcription	Osteobl	bone
9	chr3:140951800-140959000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:140951800-140960200	Weak transcription	Esophagus	oesophagus
11	chr3:140951800-140960400	Weak transcription	Brain Substantia Nigra	brain
12	chr3:140951800-140962000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:140951800-140962200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:140952000-140956600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:140952000-140956600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:140952000-140956600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:140952000-140956800	Weak transcription	HSMM	muscle
18	chr3:140952000-140957000	Weak transcription	Brain Anterior Caudate	brain
19	chr3:140952000-140958400	Weak transcription	Fetal Kidney	kidney
20	chr3:140952000-140959000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:140952000-140959000	Weak transcription	Placenta	Placenta
22	chr3:140952000-140959600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:140952000-140962000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr3:140952200-140958000	Weak transcription	Right Ventricle	heart
25	chr3:140952400-140959600	Weak transcription	Colon Smooth Muscle	Colon
26	chr3:140952600-140957800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:140953000-140956800	Enhancers	Fetal Heart	heart
28	chr3:140953000-140958800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:140953200-140959200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:140953400-140958800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:140953600-140959600	Genic enhancers	Fetal Thymus	thymus
32	chr3:140953600-140960200	Weak transcription	Spleen	Spleen
33	chr3:140953800-140956600	Weak transcription	Fetal Muscle Trunk	muscle
34	chr3:140953800-140958400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:140954000-140959200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr3:140954200-140959200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr3:140954400-140956800	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr3:140954800-140957000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:140954800-140957200	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr3:140954800-140957200	Enhancers	Primary hematopoietic stem cells	blood
41	chr3:140954800-140958600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:140955000-140956600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:140955000-140956600	Weak transcription	Pancreas	Pancrea
44	chr3:140955000-140956800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr3:140955000-140956800	Weak transcription	Lung	lung
46	chr3:140955000-140959400	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr3:140955000-140959600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:140955000-140960200	Weak transcription	Adipose Nuclei	Adipose
49	chr3:140955000-140960600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr3:140955000-140961800	Enhancers	Cortex derived primary cultured neurospheres	brain

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