Variant report

Variant	rs2314666
Chromosome Location	chr19:18689904-18689905
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18671549..18675239-chr19:18688508..18691230,4	K562	blood:
2	chr19:18631578..18634623-chr19:18688781..18690661,3	K562	blood:
3	chr19:18688171..18690449-chr19:18859750..18861413,2	MCF-7	breast:
4	chr19:18688421..18691115-chr19:18697515..18700265,3	K562	blood:
5	chr19:18631578..18633259-chr19:18688781..18690661,2	K562	blood:
6	chr19:18624925..18627602-chr19:18688802..18692839,3	K562	blood:
7	chr19:18627652..18630602-chr19:18688456..18690263,2	K562	blood:
8	chr19:18666982..18671000-chr19:18686640..18690088,4	K562	blood:
9	chr19:18645533..18647527-chr19:18689802..18691747,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000105656	Chromatin interaction
ENSG00000105700	Chromatin interaction
ENSG00000006015	Chromatin interaction
ENSG00000268030	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10409392	0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap]
rs10425018	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1043192	0.86[JPT][hapmap]
rs11086114	0.83[ASN][1000 genomes]
rs11667551	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11672297	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12150991	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12608925	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12609505	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1468475	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1862645	0.86[JPT][hapmap]
rs2057649	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2058077	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2074175	0.85[JPT][hapmap]
rs2079015	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2079016	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2238650	0.85[JPT][hapmap]
rs2283616	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2302055	1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2314664	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2314665	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2314667	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28451415	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28711754	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3170474	0.90[JPT][hapmap]
rs35867875	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35875334	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36050418	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3761032	0.86[JPT][hapmap]
rs3761034	0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3761036	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3803917	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4629093	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808137	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808821	0.87[ASN][1000 genomes]
rs4808823	0.85[JPT][hapmap]
rs4808839	0.86[JPT][hapmap]
rs55724121	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55888366	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58782998	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59798925	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62137086	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6554	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs709679	0.86[JPT][hapmap]
rs7250192	0.86[JPT][hapmap]
rs7250623	0.95[JPT][hapmap]
rs7253088	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7254004	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7256319	0.90[JPT][hapmap]
rs7258480	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7648	1.00[CHB][hapmap];0.84[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8109364	0.93[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.88[YRI][hapmap]
rs8110371	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8110374	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs916791	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers 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	71 gene(s)	inside rSNPs	diseases
5	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
6	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
7	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
8	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2314666	UBA52	cis	lymphoblastoid	seeQTL
rs2314666	CYP4F8	cis	cerebellum	SCAN
rs2314666	UBA52	cis	multi-tissue	Pritchard
rs2314666	GATAD2A	cis	cerebellum	SCAN
rs2314666	NDUFA13	cis	parietal	SCAN
rs2314666	ZNF682	cis	parietal	SCAN
rs2314666	UBA52	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18684200-18690200	Strong transcription	Fetal Brain Female	brain
2	chr19:18684400-18690200	Strong transcription	Primary T cells from cord blood	blood
3	chr19:18684400-18691400	Weak transcription	Fetal Brain Male	brain
4	chr19:18684400-18698600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr19:18684600-18690000	Strong transcription	Adipose Nuclei	Adipose
6	chr19:18684600-18690200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr19:18684600-18690200	Strong transcription	Fetal Muscle Leg	muscle
8	chr19:18684600-18698800	Weak transcription	Right Atrium	heart
9	chr19:18686200-18690000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr19:18686200-18698600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:18686800-18698400	Weak transcription	Colonic Mucosa	Colon
12	chr19:18686800-18699600	Weak transcription	Small Intestine	intestine
13	chr19:18687000-18691200	Weak transcription	HepG2	liver
14	chr19:18687000-18698600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr19:18687200-18690400	Weak transcription	Stomach Mucosa	stomach
16	chr19:18687200-18693200	Weak transcription	K562	blood
17	chr19:18687200-18693200	Weak transcription	NHDF-Ad	bronchial
18	chr19:18687200-18698600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr19:18687200-18698800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr19:18687200-18698800	Weak transcription	HSMMtube	muscle
21	chr19:18687200-18699000	Weak transcription	Aorta	Aorta
22	chr19:18687200-18699400	Weak transcription	Ovary	ovary
23	chr19:18687400-18691800	Weak transcription	HUVEC	blood vessel
24	chr19:18687400-18696200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr19:18687400-18696200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr19:18687400-18696400	Weak transcription	Primary B cells from cord blood	blood
27	chr19:18687400-18698600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr19:18687400-18698600	Weak transcription	Fetal Lung	lung
29	chr19:18687400-18698600	Weak transcription	Hela-S3	cervix
30	chr19:18687400-18698800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr19:18687400-18698800	Weak transcription	Psoas Muscle	Psoas
32	chr19:18687400-18699000	Weak transcription	Brain Substantia Nigra	brain
33	chr19:18687600-18695200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr19:18687600-18698600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr19:18687600-18698600	Weak transcription	HSMM	muscle
36	chr19:18687600-18698800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:18687800-18696200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr19:18687800-18698600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr19:18687800-18698800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr19:18687800-18698800	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr19:18687800-18699000	Weak transcription	Pancreas	Pancrea
42	chr19:18688000-18698600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:18688000-18698800	Weak transcription	Fetal Kidney	kidney
44	chr19:18688200-18696200	Weak transcription	Dnd41	blood
45	chr19:18688200-18698600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr19:18688200-18698800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr19:18688400-18692800	Weak transcription	Fetal Intestine Large	intestine
48	chr19:18688400-18696000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:18688400-18698600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr19:18688400-18698600	Weak transcription	Muscle Satellite Cultured Cells	--

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