Variant report

Variant	rs16853964
Chromosome Location	chr3:143363920-143363921
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142790255..142790841-chr3:143363451..143364029,2	MCF-7	breast:
2	chr3:143152268..143153220-chr3:143363059..143363930,4	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10513214	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10935499	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11916000	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1242076	0.83[YRI][hapmap]
rs57671316	0.87[ASN][1000 genomes]
rs58563012	0.93[ASN][1000 genomes]
rs58758962	0.87[ASN][1000 genomes]
rs73152850	0.87[ASN][1000 genomes]
rs73152852	0.89[ASN][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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv829745	chr3:143278512-143405626	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16853964	ACPL2	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143328200-143376200	Weak transcription	Ovary	ovary
2	chr3:143351600-143369800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:143354200-143373600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:143354200-143374000	Weak transcription	Esophagus	oesophagus
5	chr3:143357800-143369000	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr3:143358200-143369000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:143358400-143371200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:143360200-143369600	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr3:143361400-143373400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:143361600-143364200	Enhancers	Dnd41	blood
11	chr3:143362400-143364000	Enhancers	Muscle Satellite Cultured Cells	--
12	chr3:143362600-143364000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:143362800-143364000	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr3:143362800-143364000	Enhancers	Rectal Smooth Muscle	rectum
15	chr3:143363000-143364000	Enhancers	Colon Smooth Muscle	Colon
16	chr3:143363000-143364000	Enhancers	Fetal Lung	lung
17	chr3:143363200-143364000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:143363400-143367200	Weak transcription	Gastric	stomach
19	chr3:143363400-143369000	Weak transcription	Primary B cells from cord blood	blood
20	chr3:143363400-143371200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr3:143363400-143372800	Weak transcription	Brain Anterior Caudate	brain
22	chr3:143363400-143373800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:143363400-143373800	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:143363400-143377600	Weak transcription	NHDF-Ad	bronchial
25	chr3:143363600-143364400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:143363600-143367000	Weak transcription	HUVEC	blood vessel
27	chr3:143363600-143368600	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr3:143363600-143375400	Weak transcription	Fetal Thymus	thymus
29	chr3:143363600-143377800	Weak transcription	Adipose Nuclei	Adipose
30	chr3:143363600-143379000	Weak transcription	Fetal Muscle Leg	muscle
31	chr3:143363800-143369000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:143363800-143373800	Weak transcription	HSMMtube	muscle

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