Variant report

Variant	rs62019280
Chromosome Location	chr15:42786960-42786961
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:42786933-42788805	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr15:42786899-42788744	HUVEC	blood vessel:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:42781216..42785618-chr15:42786050..42793334,15	K562	blood:
2	chr15:42786881..42789392-chr15:42840485..42842780,2	K562	blood:
3	chr15:42785710..42787693-chr15:42866156..42868186,2	K562	blood:
4	chr15:42781833..42785082-chr15:42786422..42789177,6	MCF-7	breast:
5	chr15:42781216..42785097-chr15:42786050..42789793,8	K562	blood:

No data

Variant related genes	Relation type
SNAP23	TF binding region
ZNF106	TF binding region
ENSG00000180979	Chromatin interaction
ENSG00000159433	Chromatin interaction
ENSG00000103994	Chromatin interaction
ENSG00000137814	Chromatin interaction
ENSG00000092531	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10454692	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1048571	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11070375	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11630625	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11630681	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11633112	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11635041	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11635076	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11635889	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11636209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12438021	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12439377	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12440506	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17709596	0.85[EUR][1000 genomes]
rs17709867	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17766258	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17767264	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17767270	0.81[EUR][1000 genomes]
rs2595938	0.81[EUR][1000 genomes]
rs41315252	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56069741	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56172155	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62019282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019285	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019287	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019294	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62019312	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62019315	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62019320	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62019322	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62022315	0.81[EUR][1000 genomes]
rs62022316	0.85[EUR][1000 genomes]
rs62022318	0.86[EUR][1000 genomes]
rs7182376	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72711767	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8039240	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8042618	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv832987	chr15:42627447-42792348	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv3334708	chr15:42664344-42827738	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62019280	CEP27	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42783400-42787400	Weak transcription	Gastric	stomach
2	chr15:42783600-42787200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:42783600-42787400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:42783600-42787800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:42783600-42787800	Weak transcription	Spleen	Spleen
6	chr15:42783800-42787000	Enhancers	Primary B cells from peripheral blood	blood
7	chr15:42783800-42787000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr15:42783800-42787200	Enhancers	Placenta	Placenta
9	chr15:42783800-42787400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:42783800-42787400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:42784000-42787000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr15:42784000-42787000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:42784000-42787000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr15:42784000-42787000	Enhancers	Primary T cells fromperipheralblood	blood
15	chr15:42784000-42787000	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr15:42784000-42787000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr15:42784000-42787000	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr15:42784000-42787000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr15:42784000-42787000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:42784000-42787000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:42784000-42787000	Weak transcription	Brain Angular Gyrus	brain
22	chr15:42784000-42787000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr15:42784000-42787000	Weak transcription	Brain Germinal Matrix	brain
24	chr15:42784000-42787000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr15:42784000-42787000	Weak transcription	Brain Substantia Nigra	brain
26	chr15:42784000-42787000	Weak transcription	Fetal Brain Female	brain
27	chr15:42784000-42787000	Weak transcription	Fetal Lung	lung
28	chr15:42784000-42787000	Weak transcription	Fetal Stomach	stomach
29	chr15:42784000-42787000	Weak transcription	Right Ventricle	heart
30	chr15:42784000-42787000	Weak transcription	A549	lung
31	chr15:42784000-42787000	Weak transcription	HSMMtube	muscle
32	chr15:42784000-42787000	Enhancers	HUVEC	blood vessel
33	chr15:42784000-42787200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr15:42784000-42787200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr15:42784000-42787200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr15:42784000-42787200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr15:42784000-42787200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr15:42784000-42787200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr15:42784000-42787200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr15:42784200-42787000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr15:42784200-42787000	Weak transcription	Fetal Intestine Large	intestine
42	chr15:42784200-42787000	Weak transcription	Fetal Kidney	kidney
43	chr15:42784200-42787000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr15:42784200-42787000	Weak transcription	Small Intestine	intestine
45	chr15:42784200-42787000	Weak transcription	Thymus	Thymus
46	chr15:42784200-42787000	Weak transcription	NH-A	brain
47	chr15:42784200-42787000	Weak transcription	Osteobl	bone
48	chr15:42784200-42787200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:42784200-42787200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr15:42784200-42787400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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