Variant report

Variant	rs2302465
Chromosome Location	chr4:15709192-15709193
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXP2	chr4:15708971-15709330	SK-N-MC	brain:	n/a	n/a
2	CEBPB	chr4:15708746-15709372	Hela-S3	cervix:	n/a	chr4:15709046-15709057 chr4:15709046-15709057 chr4:15709044-15709055
3	TCF7L2	chr4:15708914-15709300	PANC-1	pancreas:	n/a	n/a
4	USF2	chr4:15709066-15709312	Hela-S3	cervix:	n/a	n/a
5	MAX	chr4:15709002-15709355	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr4:15709066-15709393	SK-N-MC	brain:	n/a	n/a
7	STAT3	chr4:15708990-15709252	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr4:15708896-15709294	Hela-S3	cervix:	n/a	n/a
9	RFX5	chr4:15709090-15709299	Hela-S3	cervix:	n/a	n/a
10	STAT3	chr4:15709016-15709270	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:15694450..15696335-chr4:15709178..15711089,2	K562	blood:

Variant related genes	Relation type
BST1	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs16892232	0.90[EUR][1000 genomes]
rs16892260	0.81[CEU][hapmap]
rs17385861	0.82[EUR][1000 genomes]
rs17385951	0.82[EUR][1000 genomes]
rs17405797	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17476642	0.91[CEU][hapmap];0.80[TSI][hapmap]
rs17476879	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs2302469	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3756245	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3822258	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4279202	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs55735476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55757331	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55784324	0.86[EUR][1000 genomes]
rs55803452	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55963737	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56065468	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56093715	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs56094420	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs56149419	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56166932	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73224650	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73224656	0.92[EUR][1000 genomes]
rs73224663	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73237171	0.82[EUR][1000 genomes]
rs73237172	0.83[EUR][1000 genomes]
rs73237182	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs73237198	0.83[EUR][1000 genomes]
rs73239165	0.83[EUR][1000 genomes]
rs73239167	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs73239174	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73239175	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73239182	0.86[EUR][1000 genomes]
rs73239189	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73239191	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73239193	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73241109	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73241111	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs73241112	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73241117	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73241120	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs73241180	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73241183	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73241185	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73241190	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73241191	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73241195	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73241197	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73241198	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73243105	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73243107	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73243112	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73243114	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73243118	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73243126	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73243128	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73243129	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73243131	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73243132	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73243135	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs955411	1.00[CHD][hapmap]

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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer 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 target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2302465	LOC285550	cis	normal skin	skin_eQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15697600-15723600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:15705000-15735200	Weak transcription	Lung	lung
3	chr4:15705200-15716200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:15705200-15716200	Weak transcription	Brain Anterior Caudate	brain
5	chr4:15705200-15720400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:15705200-15720600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:15705200-15731000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:15705400-15709200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:15705400-15709600	Weak transcription	Fetal Intestine Small	intestine
10	chr4:15705400-15713800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:15705400-15715800	Weak transcription	Fetal Lung	lung
12	chr4:15705400-15715800	Weak transcription	Fetal Stomach	stomach
13	chr4:15705400-15715800	Weak transcription	NH-A	brain
14	chr4:15705400-15716200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:15705400-15716200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:15705400-15716200	Weak transcription	A549	lung
17	chr4:15705400-15718800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:15705400-15727400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:15705600-15714000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr4:15705800-15715600	Weak transcription	Osteobl	bone
21	chr4:15705800-15716200	Weak transcription	Fetal Intestine Large	intestine
22	chr4:15705800-15719400	Weak transcription	Spleen	Spleen
23	chr4:15706000-15727800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr4:15706600-15709200	Genic enhancers	Primary monocytes fromperipheralblood	blood
25	chr4:15706800-15709400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:15706800-15710000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:15707400-15709800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr4:15707400-15711000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr4:15707400-15711800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
30	chr4:15707400-15742800	Weak transcription	Primary B cells from cord blood	blood
31	chr4:15707600-15709400	Enhancers	Adipose Nuclei	Adipose
32	chr4:15708000-15709200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:15708000-15716200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:15708200-15709200	Enhancers	Fetal Heart	heart
35	chr4:15708200-15709400	Enhancers	NHDF-Ad	bronchial
36	chr4:15708200-15710000	Enhancers	Hela-S3	cervix
37	chr4:15708400-15709400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:15708400-15709400	Enhancers	Brain Hippocampus Middle	brain
39	chr4:15708600-15709200	Enhancers	Liver	Liver
40	chr4:15708800-15709200	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr4:15708800-15709400	Enhancers	Brain Angular Gyrus	brain
42	chr4:15708800-15709400	Enhancers	Brain Substantia Nigra	brain
43	chr4:15708800-15720200	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr4:15708800-15739400	Weak transcription	Ovary	ovary
45	chr4:15709000-15710800	Weak transcription	HepG2	liver
46	chr4:15709000-15713200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr4:15709000-15716000	Weak transcription	Fetal Brain Female	brain

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