Variant report

Variant	rs2302469
Chromosome Location	chr4:15688604-15688605
allele	C/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:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:15686622..15689268-chr4:15689311..15691528,2	K562	blood:
2	chr4:15688099..15691851-chr4:15693334..15695870,4	MCF-7	breast:
3	chr17:56707290..56709152-chr4:15686738..15688828,2	MCF-7	breast:
4	chr4:15681636..15683511-chr4:15686226..15688652,2	K562	blood:
5	chr4:15680881..15687102-chr4:15687861..15693031,11	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM200B-1	chr4:15688555-15689083	NONHSAT095634
2	lnc-FAM200B-1	chr4:15688555-15688768	NONHSAT095635

No data

Variant related genes	Relation type
ENSG00000237765	Chromatin interaction
ENSG00000118564	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs16892232	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16892260	0.81[CEU][hapmap]
rs17385861	0.84[EUR][1000 genomes]
rs17385951	0.84[EUR][1000 genomes]
rs17405797	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17476642	0.91[CEU][hapmap]
rs17476879	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2302465	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];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3822258	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4279202	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs55735476	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55757331	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55784324	0.87[EUR][1000 genomes]
rs55803452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55963737	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56065468	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56093715	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs56094420	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs56149419	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56166932	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs73224650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73224656	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73224663	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73237171	0.84[EUR][1000 genomes]
rs73237172	0.85[EUR][1000 genomes]
rs73237182	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs73237198	0.85[EUR][1000 genomes]
rs73239165	0.85[EUR][1000 genomes]
rs73239167	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs73239174	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs73239175	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs73239182	0.87[EUR][1000 genomes]
rs73239189	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs73239191	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs73239193	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs73241109	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73241111	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73241112	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73241117	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73241120	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73241180	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73241183	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73241185	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73241190	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73241191	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73241195	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73241197	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73241198	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73243105	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73243107	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73243112	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73243114	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73243118	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73243126	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73243128	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73243129	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73243131	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73243132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73243135	1.00[AMR][1000 genomes];0.99[EUR][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	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
6	nsv521183	chr4:15610771-15692136	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2302469	LOC285550	cis	normal skin	skin_eQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15684000-15691000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:15684000-15692400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:15684000-15697000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:15684000-15704400	Weak transcription	Left Ventricle	heart
5	chr4:15684400-15692200	Weak transcription	Right Ventricle	heart
6	chr4:15684600-15690800	Weak transcription	HSMMtube	muscle
7	chr4:15684800-15690800	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr4:15684800-15691600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:15684800-15691600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:15684800-15692200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr4:15684800-15692400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr4:15684800-15693600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:15684800-15694200	Weak transcription	Fetal Brain Male	brain
14	chr4:15684800-15704400	Weak transcription	Aorta	Aorta
15	chr4:15685000-15690600	Weak transcription	Brain Germinal Matrix	brain
16	chr4:15685000-15691400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr4:15685000-15692000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr4:15685000-15692000	Weak transcription	Right Atrium	heart
19	chr4:15685000-15693000	Weak transcription	Psoas Muscle	Psoas
20	chr4:15685000-15695800	Weak transcription	Stomach Mucosa	stomach
21	chr4:15685800-15689400	Strong transcription	K562	blood
22	chr4:15685800-15691200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr4:15685800-15691400	Strong transcription	Fetal Thymus	thymus
24	chr4:15685800-15692000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr4:15686000-15689000	Strong transcription	Osteobl	bone
26	chr4:15686000-15692200	Weak transcription	Brain Angular Gyrus	brain
27	chr4:15686000-15692400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:15686200-15690000	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr4:15686200-15690600	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr4:15686400-15688800	Strong transcription	NHDF-Ad	bronchial
31	chr4:15686400-15689000	Genic enhancers	Primary monocytes fromperipheralblood	blood
32	chr4:15686400-15689600	Strong transcription	Primary hematopoietic stem cells	blood
33	chr4:15686400-15690400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr4:15686400-15690600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr4:15686400-15691000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:15686400-15691200	Weak transcription	Hela-S3	cervix
37	chr4:15686400-15691400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:15686400-15691800	Weak transcription	HepG2	liver
39	chr4:15686400-15692200	Weak transcription	Small Intestine	intestine
40	chr4:15686400-15692800	Weak transcription	GM12878-XiMat	blood
41	chr4:15686600-15689200	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr4:15686600-15689200	Strong transcription	HSMM	muscle
43	chr4:15686600-15691200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:15686600-15691400	Strong transcription	Fetal Intestine Large	intestine
45	chr4:15686600-15691600	Weak transcription	NHLF	lung
46	chr4:15686600-15704400	Weak transcription	Thymus	Thymus
47	chr4:15686800-15690600	Strong transcription	HUVEC	blood vessel
48	chr4:15686800-15691400	Weak transcription	Brain Substantia Nigra	brain
49	chr4:15687000-15689000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:15687000-15690800	Strong transcription	HUES64 Cell Line	embryonic stem cell

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