Variant report

Variant	rs348941
Chromosome Location	chr5:112824166-112824167
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:112810517..112812922-chr5:112822746..112824513,2	MCF-7	breast:
2	chr5:112771582..112773208-chr5:112822674..112824229,2	MCF-7	breast:
3	chr5:112815129..112817278-chr5:112821546..112824225,2	MCF-7	breast:
4	chr5:112823438..112825437-chr5:112848716..112850682,3	MCF-7	breast:
5	chr5:112823064..112825616-chr5:112827873..112829693,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TSSK1B-1	chr5:112823942-112824520	NONHSAT103267

No data

Variant related genes	Relation type
ENSG00000047188	Chromatin interaction
ENSG00000251741	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1057827	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs168365	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs168366	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs171180	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs191553	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2248930	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3097242	0.84[EUR][1000 genomes]
rs348924	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs348925	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs348926	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs348928	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs348929	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs348930	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs348931	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs348932	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs348938	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs348940	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs348944	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs348945	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348946	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs348947	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs348948	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs348951	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs348952	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs348954	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs348955	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs348956	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs348957	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs348958	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs348960	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs348961	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs348962	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs348963	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs364738	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs366219	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs367943	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs388363	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs444322	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs451425	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs451453	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs455435	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs458044	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs460079	0.84[EUR][1000 genomes]
rs463167	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs463249	0.81[EUR][1000 genomes]
rs644154	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9800375	0.83[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	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112822000-112824400	Active TSS	HMEC	breast
2	chr5:112822200-112824600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:112822600-112824600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:112822800-112824400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:112822800-112824400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr5:112822800-112824600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:112822800-112824800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
8	chr5:112822800-112825000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr5:112822800-112825200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr5:112823000-112824200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:112823000-112824200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:112823000-112824200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:112823000-112824400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:112823000-112824400	Bivalent/Poised TSS	Fetal Stomach	stomach
15	chr5:112823000-112824400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
16	chr5:112823000-112824400	Active TSS	NHEK	skin
17	chr5:112823000-112824600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr5:112823000-112824600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr5:112823000-112824600	Active TSS	Ovary	ovary
20	chr5:112823000-112824600	Active TSS	NHLF	lung
21	chr5:112823000-112824800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr5:112823000-112824800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
23	chr5:112823000-112825000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
24	chr5:112823000-112825000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
25	chr5:112823000-112825000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
26	chr5:112823000-112825000	Active TSS	Fetal Kidney	kidney
27	chr5:112823000-112825000	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr5:112823000-112825200	Active TSS	Aorta	Aorta
29	chr5:112823200-112824600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
30	chr5:112823200-112824600	Active TSS	Fetal Heart	heart
31	chr5:112823200-112824600	Active TSS	Left Ventricle	heart
32	chr5:112823200-112824600	Bivalent/Poised TSS	Thymus	Thymus
33	chr5:112823200-112824800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
34	chr5:112823200-112824800	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
35	chr5:112823200-112825200	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr5:112823400-112824200	Active TSS	Muscle Satellite Cultured Cells	--
37	chr5:112823400-112824400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:112823400-112824400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:112823400-112824400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:112823400-112824400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
41	chr5:112823400-112824400	Active TSS	Colon Smooth Muscle	Colon
42	chr5:112823400-112824400	Active TSS	HSMMtube	muscle
43	chr5:112823400-112824600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr5:112823400-112824600	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
45	chr5:112823400-112824600	Flanking Bivalent TSS/Enh	Lung	lung
46	chr5:112823400-112824800	Active TSS	H9 Cell Line	embryonic stem cell
47	chr5:112823400-112824800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
48	chr5:112823400-112824800	Active TSS	Brain Substantia Nigra	brain
49	chr5:112823400-112824800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
50	chr5:112823400-112825000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell

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