Variant report

Variant	rs2724725
Chromosome Location	chr3:137887747-137887748
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:137886831..137889981-chr3:137890698..137894994,6	MCF-7	breast:
2	chr3:137880775..137882783-chr3:137887476..137889731,2	K562	blood:
3	chr3:137886740..137888372-chr3:137892285..137893890,2	K562	blood:

Variant related genes	Relation type
ENSG00000138231	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1137760	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712078	0.88[ASN][1000 genomes]
rs12185936	0.83[ASN][1000 genomes]
rs1600697	0.84[EUR][1000 genomes]
rs2219936	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2251550	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2346744	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346745	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346747	0.81[EUR][1000 genomes]
rs2622694	0.82[EUR][1000 genomes]
rs2622696	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2622699	0.82[EUR][1000 genomes]
rs2622700	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622732	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2622733	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622734	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2622735	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622736	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2622737	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2622739	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2622740	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2622741	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2622742	0.84[EUR][1000 genomes]
rs2622743	0.84[EUR][1000 genomes]
rs2622744	0.82[EUR][1000 genomes]
rs2724681	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2724690	0.83[EUR][1000 genomes]
rs2724691	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2724692	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2724710	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2724711	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2724712	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2724726	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2724727	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329380	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732839	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs608594	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7430414	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7613041	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7613558	0.82[EUR][1000 genomes]
rs7632402	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs774803	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs774804	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs774805	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs774806	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs774807	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774808	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774809	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774810	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774811	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774812	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774813	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774814	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs811810	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs811811	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827617	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9840008	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9851548	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2757890	chr3:137611789-137933835	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2759180	chr3:137611789-137933835	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2751978	chr3:137715302-137890750	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv2762347	chr3:137851198-137910007	Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv998106	chr3:137851198-137934610	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv877536	chr3:137870523-137970907	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2724725	A4GNT	cis	Thyroid	GTEx
rs2724725	DBR1	Cis_1M	lymphoblastoid	RTeQTL
rs2724725	A4GNT	cis	Skin Sun Exposed Lower leg	GTEx
rs2724725	A4GNT	cis	Nerve Tibial	GTEx
rs2724725	A4GNT	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137876000-137892400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:137876400-137892800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:137878800-137892200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:137879000-137888200	Strong transcription	Fetal Brain Female	brain
5	chr3:137879000-137888400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:137879000-137888600	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr3:137879000-137889600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:137879000-137890000	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:137879000-137891000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr3:137879000-137891200	Weak transcription	Fetal Brain Male	brain
11	chr3:137879000-137891400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:137879000-137891600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:137879200-137888800	Strong transcription	Fetal Intestine Large	intestine
14	chr3:137879200-137889000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:137879200-137889000	Weak transcription	Hela-S3	cervix
16	chr3:137879200-137889200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:137879200-137889600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:137879200-137889600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:137879200-137889600	Strong transcription	Left Ventricle	heart
20	chr3:137879200-137890200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:137879200-137890200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:137879200-137890200	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr3:137879200-137890800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr3:137879200-137891000	Strong transcription	Adipose Nuclei	Adipose
25	chr3:137879200-137891000	Strong transcription	Fetal Lung	lung
26	chr3:137879200-137891200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:137879200-137891400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:137879200-137891600	Strong transcription	Liver	Liver
29	chr3:137879200-137891800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:137879200-137892000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:137879200-137892200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:137879200-137892400	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:137879400-137888200	Strong transcription	Brain Germinal Matrix	brain
34	chr3:137879400-137888800	Strong transcription	Fetal Stomach	stomach
35	chr3:137879400-137889200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:137879400-137892200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr3:137879600-137890400	Weak transcription	K562	blood
38	chr3:137879600-137892200	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr3:137879600-137892200	Weak transcription	A549	lung
40	chr3:137879800-137891600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:137880000-137891200	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr3:137880000-137891200	Strong transcription	Primary B cells from peripheral blood	blood
43	chr3:137880000-137891400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr3:137880200-137889000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr3:137880200-137891200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr3:137880400-137888800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr3:137880400-137889400	Strong transcription	Primary T cells from cord blood	blood
48	chr3:137880400-137890400	Strong transcription	Fetal Muscle Leg	muscle
49	chr3:137880400-137890800	Strong transcription	Fetal Thymus	thymus
50	chr3:137880600-137888200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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