Variant report

Variant	rs4578216
Chromosome Location	chr1:154900721-154900722
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154900011..154901853-chr1:154902099..154904633,2	K562	blood:
2	chr1:154898235..154901103-chr1:154908518..154910078,2	K562	blood:
3	chr1:154578327..154580689-chr1:154898287..154900817,2	MCF-7	breast:
4	chr1:154898414..154901108-chr1:154965094..154967313,2	MCF-7	breast:
5	chr1:154881013..154882772-chr1:154900438..154902039,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160710	Chromatin interaction
ENSG00000163344	Chromatin interaction
ENSG00000270361	Chromatin interaction
ENSG00000163352	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1007170	0.90[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs10796935	0.90[ASN][1000 genomes]
rs10908446	0.84[ASN][1000 genomes]
rs10908447	0.84[ASN][1000 genomes]
rs10908448	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs1109815	0.86[ASN][1000 genomes]
rs11264278	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11264280	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11264281	0.84[ASN][1000 genomes]
rs11264282	0.84[ASN][1000 genomes]
rs11264283	0.84[ASN][1000 genomes]
rs11264284	0.86[ASN][1000 genomes]
rs11264290	0.86[ASN][1000 genomes]
rs12036859	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs12087657	0.81[GIH][hapmap];0.93[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs12095061	0.86[ASN][1000 genomes]
rs12130132	0.90[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs1580943	0.89[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs1976559	0.90[ASN][1000 genomes]
rs1977879	0.90[ASN][1000 genomes]
rs2061690	0.90[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2102423	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs2135219	0.84[ASN][1000 genomes]
rs2174507	0.90[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs2335407	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap]
rs2335408	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs2335409	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs3738026	0.90[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4240874	0.90[ASN][1000 genomes]
rs4240875	0.90[ASN][1000 genomes]
rs4339857	0.90[ASN][1000 genomes]
rs4845398	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs4845400	0.84[ASN][1000 genomes]
rs4845677	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs4845678	0.84[ASN][1000 genomes]
rs4845679	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs4845680	0.84[ASN][1000 genomes]
rs4845682	0.86[ASN][1000 genomes]
rs4845683	0.86[ASN][1000 genomes]
rs4845685	0.85[ASN][1000 genomes]
rs4845687	0.87[ASN][1000 genomes]
rs4845688	0.90[ASN][1000 genomes]
rs4845689	0.90[ASN][1000 genomes]
rs4845690	0.90[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs4845691	0.90[ASN][1000 genomes]
rs4845693	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4845694	0.86[ASN][1000 genomes]
rs4845695	0.90[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs4845696	0.86[ASN][1000 genomes]
rs6656435	0.86[ASN][1000 genomes]
rs6674853	0.90[ASN][1000 genomes]
rs6686873	0.86[ASN][1000 genomes]
rs6699043	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs705094	0.90[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs72702224	0.86[ASN][1000 genomes]
rs7528532	0.84[ASN][1000 genomes]
rs7531728	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap]
rs7553195	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap]
rs869506	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs877343	0.90[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs883718	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs906593	0.90[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs9427170	0.86[LWK][hapmap];0.82[YRI][hapmap]
rs9793588	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv432942	chr1:154818353-154903047	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv464073	chr1:154837796-154904840	Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv547960	chr1:154837796-154904840	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv2977	chr1:154881053-154907613	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4578216	OAZ3	cis	parietal	SCAN
rs4578216	KCNN3	cis	cerebellum	SCAN
rs4578216	LCE2C	cis	parietal	SCAN
rs4578216	SNAPIN	cis	cerebellum	SCAN
rs4578216	C1orf189	cis	cerebellum	SCAN
rs4578216	LENEP	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154884800-154908400	Weak transcription	Psoas Muscle	Psoas
2	chr1:154886800-154908200	Weak transcription	Fetal Heart	heart
3	chr1:154889800-154900800	Weak transcription	HepG2	liver
4	chr1:154891200-154908600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:154892600-154903600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:154892600-154905400	Strong transcription	Fetal Muscle Leg	muscle
7	chr1:154893200-154902800	Strong transcription	Liver	Liver
8	chr1:154893200-154905600	Strong transcription	Stomach Smooth Muscle	stomach
9	chr1:154893200-154908200	Weak transcription	NH-A	brain
10	chr1:154893400-154901200	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:154893400-154902600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:154893400-154905600	Strong transcription	Fetal Stomach	stomach
13	chr1:154893800-154903800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:154893800-154904000	Weak transcription	Stomach Mucosa	stomach
15	chr1:154894200-154901800	Strong transcription	Brain Cingulate Gyrus	brain
16	chr1:154894200-154902600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr1:154894200-154905000	Strong transcription	Fetal Brain Female	brain
18	chr1:154894400-154904800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:154894400-154908400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:154894600-154902400	Strong transcription	Gastric	stomach
21	chr1:154894600-154903600	Strong transcription	Fetal Intestine Small	intestine
22	chr1:154894600-154905000	Strong transcription	Fetal Muscle Trunk	muscle
23	chr1:154894800-154901600	Strong transcription	Right Ventricle	heart
24	chr1:154894800-154902400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:154894800-154902400	Strong transcription	Aorta	Aorta
26	chr1:154894800-154902400	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr1:154894800-154902400	Strong transcription	Brain Substantia Nigra	brain
28	chr1:154894800-154902400	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr1:154894800-154902600	Strong transcription	Brain Angular Gyrus	brain
30	chr1:154894800-154902600	Strong transcription	Lung	lung
31	chr1:154894800-154902600	Strong transcription	Rectal Smooth Muscle	rectum
32	chr1:154894800-154902600	Strong transcription	Spleen	Spleen
33	chr1:154894800-154903400	Strong transcription	Fetal Intestine Large	intestine
34	chr1:154894800-154904800	Strong transcription	Esophagus	oesophagus
35	chr1:154894800-154904800	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr1:154894800-154905000	Strong transcription	Adipose Nuclei	Adipose
37	chr1:154894800-154905000	Strong transcription	Brain Germinal Matrix	brain
38	chr1:154894800-154905000	Strong transcription	GM12878-XiMat	blood
39	chr1:154895000-154900800	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr1:154895000-154901800	Strong transcription	Ovary	ovary
41	chr1:154895000-154901800	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:154895000-154902600	Strong transcription	Brain Anterior Caudate	brain
43	chr1:154895000-154902600	Strong transcription	Placenta	Placenta
44	chr1:154895000-154905000	Strong transcription	Brain Hippocampus Middle	brain
45	chr1:154895000-154907600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr1:154895400-154902000	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr1:154895800-154902600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:154895800-154904600	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:154895800-154904600	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:154895800-154908000	Weak transcription	Fetal Brain Male	brain

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