Variant report

Variant	rs2724727
Chromosome Location	chr3:137889919-137889920
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:137889293..137890860-chr3:137969954..137972677,2	K562	blood:
2	chr3:137889244..137891062-chr3:137891695..137893899,3	K562	blood:
3	chr3:137886831..137889981-chr3:137890698..137894994,6	MCF-7	breast:
4	chr3:137889024..137895470-chr3:137896789..137909029,20	K562	blood:
5	chr3:137883514..137885289-chr3:137888443..137890790,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114098	Chromatin interaction
ENSG00000138231	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1137760	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712078	0.88[ASN][1000 genomes]
rs12185936	0.83[ASN][1000 genomes]
rs1600697	0.82[EUR][1000 genomes]
rs2170309	0.81[CEU][hapmap]
rs2219936	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[EUR][1000 genomes]
rs2246945	0.81[CEU][hapmap]
rs2251550	0.80[EUR][1000 genomes]
rs2346744	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346745	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346747	0.95[CEU][hapmap];0.90[CHB][hapmap]
rs2622694	0.95[CEU][hapmap];0.90[CHB][hapmap];0.80[EUR][1000 genomes]
rs2622695	0.81[CEU][hapmap]
rs2622699	0.80[EUR][1000 genomes]
rs2622700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622732	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2622733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2622735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622736	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2622737	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2622739	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2622740	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2622741	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2622742	0.82[EUR][1000 genomes]
rs2622743	0.82[EUR][1000 genomes]
rs2622744	0.81[EUR][1000 genomes]
rs2724681	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2724690	0.81[EUR][1000 genomes]
rs2724691	0.95[CEU][hapmap];0.85[CHB][hapmap];0.80[EUR][1000 genomes]
rs2724692	0.95[CEU][hapmap];0.90[CHB][hapmap];0.80[EUR][1000 genomes]
rs2724710	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2724711	0.81[EUR][1000 genomes]
rs2724712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2724725	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2724726	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329380	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732839	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs608594	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7430414	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7613041	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7613558	0.80[EUR][1000 genomes]
rs7632402	0.82[EUR][1000 genomes]
rs774803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs774804	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs774805	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs774806	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs774807	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774808	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774809	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774810	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774811	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774812	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774813	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774814	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs811810	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs811811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827617	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9840008	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9851548	0.95[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2724727	DBR1	Cis_1M	lymphoblastoid	RTeQTL
rs2724727	A4GNT	cis	Artery Tibial	GTEx
rs2724727	A4GNT	cis	Nerve Tibial	GTEx
rs2724727	DBR1	cis	normal skin	skin_eQTL
rs2724727	A4GNT	cis	Skin Sun Exposed Lower leg	GTEx
rs2724727	A4GNT	cis	Thyroid	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	chr3:137879000-137890000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr3:137879000-137891000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr3:137879000-137891200	Weak transcription	Fetal Brain Male	brain
7	chr3:137879000-137891400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:137879000-137891600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:137879200-137890200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:137879200-137890200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:137879200-137890200	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr3:137879200-137890800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr3:137879200-137891000	Strong transcription	Adipose Nuclei	Adipose
14	chr3:137879200-137891000	Strong transcription	Fetal Lung	lung
15	chr3:137879200-137891200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:137879200-137891400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:137879200-137891600	Strong transcription	Liver	Liver
18	chr3:137879200-137891800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:137879200-137892000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:137879200-137892200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:137879200-137892400	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:137879400-137892200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr3:137879600-137890400	Weak transcription	K562	blood
24	chr3:137879600-137892200	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:137879600-137892200	Weak transcription	A549	lung
26	chr3:137879800-137891600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:137880000-137891200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr3:137880000-137891200	Strong transcription	Primary B cells from peripheral blood	blood
29	chr3:137880000-137891400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:137880200-137891200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:137880400-137890400	Strong transcription	Fetal Muscle Leg	muscle
32	chr3:137880400-137890800	Strong transcription	Fetal Thymus	thymus
33	chr3:137880600-137890600	Strong transcription	Dnd41	blood
34	chr3:137880600-137891400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:137880600-137891400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:137880600-137891800	Strong transcription	Fetal Muscle Trunk	muscle
37	chr3:137880800-137890400	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr3:137880800-137891200	Strong transcription	Placenta	Placenta
39	chr3:137880800-137892800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr3:137881200-137892400	Weak transcription	Stomach Mucosa	stomach
41	chr3:137881400-137892200	Weak transcription	Small Intestine	intestine
42	chr3:137882200-137892400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:137882200-137892400	Weak transcription	Pancreas	Pancrea
44	chr3:137882200-137892800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:137882200-137892800	Weak transcription	Aorta	Aorta
46	chr3:137883600-137891800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:137884400-137890200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr3:137884800-137891600	Strong transcription	Osteobl	bone
49	chr3:137885200-137891200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:137885800-137890600	Weak transcription	HUVEC	blood vessel

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