Variant report

Variant	rs3731812
Chromosome Location	chr2:86732576-86732577
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86730870..86733454-chr2:86738287..86740838,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115561	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1015117	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10169746	0.81[ASN][1000 genomes]
rs10180036	0.81[EUR][1000 genomes]
rs10184879	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10187880	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1020306	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1080551	0.81[ASN][1000 genomes]
rs11127045	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11127046	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1137684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676576	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11684230	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11689330	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12328637	0.82[EUR][1000 genomes]
rs12613282	0.83[EUR][1000 genomes]
rs12614447	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12615285	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12714184	0.81[EUR][1000 genomes]
rs12714186	0.81[EUR][1000 genomes]
rs12714188	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12714199	0.81[ASN][1000 genomes]
rs12987172	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12991654	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13015620	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13034615	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13390713	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13408041	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13429696	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1465813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1518807	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1629293	0.80[ASN][1000 genomes]
rs2241803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2292887	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2367574	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3201448	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34666164	0.81[ASN][1000 genomes]
rs3755002	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3770058	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4832040	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4832041	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4832042	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4832296	0.84[ASN][1000 genomes]
rs4832297	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4832299	0.85[EUR][1000 genomes]
rs4832300	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4832302	0.81[ASN][1000 genomes]
rs4832304	0.82[EUR][1000 genomes]
rs62147239	0.80[ASN][1000 genomes]
rs6725080	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6738663	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6750226	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7369138	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570640	0.81[ASN][1000 genomes]
rs7593151	0.84[ASN][1000 genomes]
rs7596717	0.84[ASN][1000 genomes]
rs7601115	0.81[EUR][1000 genomes]
rs8179729	0.84[ASN][1000 genomes]
rs9284788	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs958561	0.81[EUR][1000 genomes]
rs9789777	0.89[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	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3731812	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86679800-86757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:86709200-86737400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:86719800-86734600	Weak transcription	Psoas Muscle	Psoas
4	chr2:86724600-86737800	Strong transcription	Stomach Smooth Muscle	stomach
5	chr2:86725400-86733200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:86726400-86735400	Weak transcription	NHLF	lung
7	chr2:86726400-86737400	Weak transcription	HUVEC	blood vessel
8	chr2:86726400-86741800	Weak transcription	NH-A	brain
9	chr2:86726400-86753000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:86726600-86736400	Weak transcription	NHDF-Ad	bronchial
11	chr2:86726600-86748600	Weak transcription	Hela-S3	cervix
12	chr2:86726800-86739000	Weak transcription	K562	blood
13	chr2:86727000-86737200	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr2:86727400-86734400	Weak transcription	Fetal Heart	heart
15	chr2:86727600-86732600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:86727600-86734600	Weak transcription	HMEC	breast
17	chr2:86728000-86732600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr2:86728000-86734200	Weak transcription	HSMM	muscle
19	chr2:86728000-86737600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:86728000-86737600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:86728000-86737600	Strong transcription	Adipose Nuclei	Adipose
22	chr2:86728000-86737800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:86728000-86737800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:86728000-86737800	Strong transcription	Fetal Intestine Large	intestine
25	chr2:86728000-86738000	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr2:86728000-86738400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:86728200-86737800	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr2:86728200-86737800	Weak transcription	Stomach Mucosa	stomach
29	chr2:86728200-86738400	Strong transcription	Dnd41	blood
30	chr2:86728200-86755800	Weak transcription	Fetal Brain Male	brain
31	chr2:86728400-86736200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:86728400-86737800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:86728400-86738000	Strong transcription	Liver	Liver
34	chr2:86728400-86738400	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr2:86728400-86738400	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr2:86728400-86738400	Strong transcription	A549	lung
37	chr2:86728400-86747200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr2:86728600-86737600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr2:86728600-86738200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:86728600-86738800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr2:86728800-86737400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:86728800-86737800	Strong transcription	Duodenum Mucosa	Duodenum
43	chr2:86728800-86737800	Strong transcription	Placenta	Placenta
44	chr2:86729000-86734800	Weak transcription	Right Ventricle	heart
45	chr2:86729000-86736400	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:86729000-86737400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:86729000-86737800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr2:86729000-86738000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr2:86729000-86738000	Strong transcription	Thymus	Thymus
50	chr2:86729000-86738200	Strong transcription	Fetal Muscle Trunk	muscle

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