Variant report

Variant	rs55715288
Chromosome Location	chr3:141108338-141108339
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141107718..141109418-chr3:141117373..141119105,2	K562	blood:
2	chr3:141105739..141107657-chr3:141108132..141110695,3	K562	blood:
3	chr3:141106008..141109150-chr3:141119369..141122507,3	MCF-7	breast:
4	chr3:141086200..141088543-chr3:141107972..141110078,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACPL2-3	chr3:141105714-141108679	NONHSAT092429

Variant related genes	Relation type
ENSG00000177311	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1344673	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16851397	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55750762	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56243018	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6763780	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73872717	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73872719	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141089200-141115800	Weak transcription	Psoas Muscle	Psoas
2	chr3:141094800-141112200	Weak transcription	Spleen	Spleen
3	chr3:141096000-141111000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:141098600-141115200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:141099000-141110400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:141099600-141109800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:141100600-141112400	Weak transcription	Lung	lung
8	chr3:141102800-141111800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:141102800-141112000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:141103200-141111000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:141103600-141110200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:141103800-141109000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:141104000-141108800	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr3:141104000-141109600	Active TSS	Brain Anterior Caudate	brain
15	chr3:141104800-141108400	Active TSS	Stomach Smooth Muscle	stomach
16	chr3:141105200-141110200	Weak transcription	Fetal Heart	heart
17	chr3:141105800-141110200	Weak transcription	Right Atrium	heart
18	chr3:141105800-141111200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:141106000-141108800	Active TSS	Duodenum Mucosa	Duodenum
20	chr3:141106000-141109200	Active TSS	Fetal Brain Female	brain
21	chr3:141106000-141109800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:141106000-141110200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:141106000-141110200	Weak transcription	Fetal Kidney	kidney
24	chr3:141106000-141111000	Weak transcription	Gastric	stomach
25	chr3:141106000-141112200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr3:141106000-141115400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:141106000-141115800	Weak transcription	Right Ventricle	heart
28	chr3:141106000-141117000	Strong transcription	Fetal Intestine Large	intestine
29	chr3:141106000-141119000	Weak transcription	Colonic Mucosa	Colon
30	chr3:141106400-141109600	Weak transcription	Fetal Intestine Small	intestine
31	chr3:141106400-141110200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:141106600-141110000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:141106600-141110200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:141106600-141111400	Weak transcription	Fetal Stomach	stomach
35	chr3:141106600-141113600	Weak transcription	K562	blood
36	chr3:141106800-141108400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:141106800-141108400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:141106800-141108600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr3:141106800-141108800	Active TSS	Fetal Brain Male	brain
40	chr3:141106800-141108800	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr3:141106800-141109000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:141106800-141110200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:141106800-141110200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr3:141106800-141110800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr3:141106800-141111200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr3:141106800-141111200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr3:141106800-141111800	Weak transcription	Placenta	Placenta
48	chr3:141106800-141114800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr3:141106800-141119200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr3:141107200-141108400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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