Variant report

Variant	rs3794568
Chromosome Location	chr15:52642199-52642200
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52640299..52642947-chr15:52856133..52857726,2	MCF-7	breast:
2	chr15:52626828..52629025-chr15:52639618..52642359,2	MCF-7	breast:
3	chr15:52547210..52549304-chr15:52640088..52643022,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128833	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10518684	1.00[ASN][1000 genomes]
rs10518689	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10518691	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1058219	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10851514	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10851515	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10851516	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10851517	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11852261	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11852555	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11853237	0.80[EUR][1000 genomes]
rs11853337	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11853455	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11853586	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11853802	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11853875	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11854130	0.81[EUR][1000 genomes]
rs11854456	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11854498	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11854886	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11855252	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11855257	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11855295	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11855584	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11855640	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11855820	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11855884	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11856242	0.81[AMR][1000 genomes]
rs11856752	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11856810	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11856896	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11858031	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11858927	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12050602	0.83[ASN][1000 genomes]
rs12050717	0.88[ASN][1000 genomes]
rs1464965	0.81[EUR][1000 genomes]
rs1464966	0.81[EUR][1000 genomes]
rs1474435	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1474436	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1474437	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1474438	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1724578	0.96[EUR][1000 genomes]
rs1724579	0.96[EUR][1000 genomes]
rs1724590	0.83[EUR][1000 genomes]
rs17541809	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17613587	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17613607	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17613951	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17651212	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17651218	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17651230	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17651242	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17651397	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17707338	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17707651	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17707705	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17707729	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1815176	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1869126	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1869127	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1869128	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2049519	0.80[EUR][1000 genomes]
rs2049520	0.81[EUR][1000 genomes]
rs2140962	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2290334	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2414148	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2414152	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28680872	0.82[EUR][1000 genomes]
rs35943650	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36074938	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3751619	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3751620	0.85[EUR][1000 genomes]
rs3816449	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4341694	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4774623	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4776044	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4776045	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55706220	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55722736	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55978431	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56039749	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56128753	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56136255	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56148029	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56227135	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56312354	0.94[ASN][1000 genomes]
rs56315558	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56332522	0.81[EUR][1000 genomes]
rs56360952	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56749732	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56850880	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56992654	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57505385	0.80[EUR][1000 genomes]
rs58043289	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58922508	0.81[EUR][1000 genomes]
rs59496859	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59584964	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60248452	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60512163	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66674706	0.81[EUR][1000 genomes]
rs67249415	0.81[EUR][1000 genomes]
rs67283829	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67399033	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67438240	0.83[ASN][1000 genomes]
rs68101123	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs68155341	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72623980	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72623982	0.80[EUR][1000 genomes]
rs72736668	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72736669	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72736696	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72736701	0.81[EUR][1000 genomes]
rs72736702	0.81[EUR][1000 genomes]
rs940966	0.96[EUR][1000 genomes]
rs940967	0.96[EUR][1000 genomes]
rs940971	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs940972	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs940973	0.83[AMR][1000 genomes];0.86[EUR][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	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3794568	KIAA1370	Cis_1M	lymphoblastoid	RTeQTL
rs3794568	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL
rs3794568	MYO5A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52597800-52643400	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr15:52600800-52646600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr15:52601000-52643400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr15:52607800-52657800	Weak transcription	Small Intestine	intestine
5	chr15:52609800-52677600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:52610000-52643400	Weak transcription	Placenta	Placenta
7	chr15:52611600-52650200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:52611800-52675800	Weak transcription	Gastric	stomach
9	chr15:52613000-52642600	Weak transcription	Colon Smooth Muscle	Colon
10	chr15:52613600-52666600	Weak transcription	Right Ventricle	heart
11	chr15:52614800-52642600	Weak transcription	Esophagus	oesophagus
12	chr15:52614800-52653200	Weak transcription	Colonic Mucosa	Colon
13	chr15:52620000-52652200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:52620600-52659200	Weak transcription	Fetal Lung	lung
15	chr15:52621200-52666600	Weak transcription	Fetal Brain Male	brain
16	chr15:52621800-52662200	Weak transcription	Psoas Muscle	Psoas
17	chr15:52623800-52644200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr15:52624600-52642400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr15:52627000-52646600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr15:52630600-52684800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr15:52631600-52679200	Weak transcription	Fetal Intestine Small	intestine
22	chr15:52632600-52643200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr15:52632600-52643400	Weak transcription	Lung	lung
24	chr15:52632600-52644200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:52632600-52670400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr15:52632800-52642600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr15:52632800-52642600	Weak transcription	NHEK	skin
28	chr15:52632800-52657400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr15:52632800-52662200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr15:52633000-52643800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr15:52633600-52645400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr15:52633600-52662200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr15:52633800-52642800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr15:52633800-52643200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr15:52635200-52648200	Strong transcription	Primary B cells from peripheral blood	blood
36	chr15:52636000-52643400	Weak transcription	Right Atrium	heart
37	chr15:52636400-52642600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr15:52636800-52642600	Weak transcription	NH-A	brain
39	chr15:52637000-52642600	Weak transcription	A549	lung
40	chr15:52638000-52671600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr15:52638200-52645800	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr15:52638800-52642600	Weak transcription	Brain Substantia Nigra	brain
43	chr15:52639400-52644600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr15:52640200-52642600	Enhancers	HSMMtube	muscle
45	chr15:52640200-52644600	Strong transcription	GM12878-XiMat	blood
46	chr15:52640200-52646200	Strong transcription	Brain Cingulate Gyrus	brain
47	chr15:52640200-52646200	Strong transcription	Fetal Brain Female	brain
48	chr15:52640200-52646400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:52640200-52646600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr15:52640200-52647000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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