Variant report

Variant	rs2546473
Chromosome Location	chr5:114961656-114961657
allele	A/C/G/T
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:41925001..41925753-chr5:114961284..114961954,2	Hela-S3	cervix:
2	chr5:114880215..114881730-chr5:114959993..114961960,2	K562	blood:
3	chr5:114936247..114938177-chr5:114959534..114962655,3	K562	blood:
4	chr5:114934797..114939548-chr5:114953575..114961976,8	K562	blood:
5	chr15:60770798..60771587-chr5:114961301..114962097,2	Hela-S3	cervix:
6	chr5:114960865..114962954-chr5:115170753..115172835,2	MCF-7	breast:
7	chr5:114960793..114963745-chr5:114966203..114968929,3	MCF-7	breast:
8	chr5:114823713..114825523-chr5:114959295..114961713,2	K562	blood:
9	chr5:114630838..114633826-chr5:114960976..114962823,3	MCF-7	breast:
10	chr5:114959789..114964126-chr5:115174280..115179155,11	MCF-7	breast:
11	chr5:114630095..114632050-chr5:114960167..114962829,2	MCF-7	breast:
12	chr5:114960090..114964183-chr5:115419193..115421485,4	MCF-7	breast:
13	chr5:114959625..114963439-chr5:115175786..115178902,4	MCF-7	breast:
14	chr5:114961103..114964725-chr5:115175944..115179319,4	K562	blood:
15	chr5:114961228..114962989-chr5:115170828..115173503,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000249249	Chromatin interaction
ENSG00000145782	Chromatin interaction
ENSG00000145780	Chromatin interaction
ENSG00000177879	Chromatin interaction
ENSG00000243414	Chromatin interaction
ENSG00000164221	Chromatin interaction
ENSG00000271918	Chromatin interaction
ENSG00000145781	Chromatin interaction
ENSG00000134970	Chromatin interaction
ENSG00000249944	Chromatin interaction
ENSG00000128915	Chromatin interaction
ENSG00000151876	Chromatin interaction
ENSG00000245534	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11740401	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11743277	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1363550	0.84[AMR][1000 genomes]
rs1422641	0.84[AMR][1000 genomes]
rs1422642	0.84[AMR][1000 genomes]
rs1422643	0.84[AMR][1000 genomes]
rs1422644	0.84[AMR][1000 genomes]
rs1592942	0.84[AMR][1000 genomes]
rs1592943	0.84[AMR][1000 genomes]
rs17138030	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs185379	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1895283	0.84[AMR][1000 genomes]
rs194398	0.97[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1978441	0.87[AMR][1000 genomes]
rs2052504	0.84[AMR][1000 genomes]
rs2052505	0.84[AMR][1000 genomes]
rs2288384	0.91[ASN][1000 genomes]
rs2431600	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2546483	0.84[AMR][1000 genomes]
rs256946	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs256960	1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs256961	1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs256966	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs256973	0.97[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs256974	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs256975	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs256979	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs256981	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs256982	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs256983	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs256985	0.97[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs256992	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2597	0.90[ASN][1000 genomes]
rs2617441	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs34986301	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4920867	0.90[ASN][1000 genomes]
rs4920869	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4920873	0.89[EUR][1000 genomes]
rs57010629	0.96[ASN][1000 genomes]
rs57028257	0.85[EUR][1000 genomes]
rs58301336	0.87[EUR][1000 genomes]
rs72817155	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73254600	0.96[ASN][1000 genomes]
rs73264735	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73782714	0.96[ASN][1000 genomes]
rs7702747	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9326965	0.84[AMR][1000 genomes]
rs9968571	0.98[AFR][1000 genomes];0.97[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	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114958800-114962400	Active TSS	Aorta	Aorta
2	chr5:114959200-114962400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:114959400-114962400	Active TSS	Fetal Intestine Large	intestine
4	chr5:114959400-114962400	Active TSS	Left Ventricle	heart
5	chr5:114959600-114962600	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr5:114959600-114962800	Active TSS	GM12878-XiMat	blood
7	chr5:114959800-114962400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:114960000-114962400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:114960000-114962400	Active TSS	Lung	lung
10	chr5:114960000-114962400	Active TSS	Pancreas	Pancrea
11	chr5:114960000-114962400	Active TSS	NHDF-Ad	bronchial
12	chr5:114960000-114962600	Active TSS	H9 Cell Line	embryonic stem cell
13	chr5:114960000-114962600	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr5:114960000-114962600	Active TSS	Stomach Mucosa	stomach
15	chr5:114960200-114961800	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr5:114960200-114962400	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr5:114960200-114962400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:114960200-114962400	Active TSS	Muscle Satellite Cultured Cells	--
19	chr5:114960200-114962400	Active TSS	Gastric	stomach
20	chr5:114960200-114962400	Active TSS	NHLF	lung
21	chr5:114960200-114962600	Active TSS	H1 Cell Line	embryonic stem cell
22	chr5:114960200-114962600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:114960200-114962600	Active TSS	Fetal Muscle Trunk	muscle
24	chr5:114960200-114962600	Active TSS	HSMMtube	muscle
25	chr5:114960400-114962400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr5:114960400-114962400	Active TSS	Ovary	ovary
27	chr5:114960400-114962400	Active TSS	HMEC	breast
28	chr5:114960400-114962600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:114960400-114962600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr5:114960400-114962600	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr5:114960400-114962600	Active TSS	Placenta	Placenta
32	chr5:114960400-114962600	Active TSS	HSMM	muscle
33	chr5:114960400-114962600	Active TSS	K562	blood
34	chr5:114960600-114962200	Active TSS	NHEK	skin
35	chr5:114960600-114962400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr5:114960600-114962400	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr5:114960600-114962400	Active TSS	Fetal Intestine Small	intestine
38	chr5:114960600-114962400	Active TSS	Psoas Muscle	Psoas
39	chr5:114960600-114962400	Active TSS	Small Intestine	intestine
40	chr5:114960600-114962400	Active TSS	A549	lung
41	chr5:114960600-114962600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr5:114960600-114962600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr5:114960600-114962600	Active TSS	Fetal Muscle Leg	muscle
44	chr5:114960600-114962600	Active TSS	Right Ventricle	heart
45	chr5:114960600-114962600	Active TSS	Stomach Smooth Muscle	stomach
46	chr5:114960600-114962600	Bivalent/Poised TSS	HepG2	liver
47	chr5:114960600-114962600	Active TSS	Osteobl	bone
48	chr5:114960800-114962200	Active TSS	Primary T cells fromperipheralblood	blood
49	chr5:114960800-114962200	Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr5:114960800-114962200	Active TSS	Rectal Mucosa Donor 31	rectum

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