Variant report

Variant	rs72685338
Chromosome Location	chr1:78358463-78358464
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:78358425-78358475	T-47D	breast:	n/a
2	chr1:78358425-78358475	PFSK-1	brain:	n/a
3	chr1:78358425-78358475	SAEC	small airway:	n/a
4	chr1:78358425-78358475	LNCaP	prostate:	n/a
5	chr1:78358425-78358475	HRE	kidney:	n/a
6	chr1:78358425-78358475	AG04450	lung:	fetal
7	chr1:78358425-78358475	NHBE	bronchial:	n/a
8	chr1:78358425-78358475	NB4	blood:	n/a
9	chr1:78358425-78358475	IMR90	lung:	fetal
10	chr1:78358425-78358475	PANC-1	pancreas:	n/a
11	chr1:78358425-78358475	Caco-2	colon:	n/a
12	chr1:78358425-78358475	GM06990	blood:	n/a
13	chr1:78358425-78358475	ECC-1	luminal epithelium:	n/a
14	chr1:78358425-78358475	HAEpiC	amniotic membrane:	n/a
15	chr1:78358425-78358475	HCM	heart:	n/a
16	chr1:78358425-78358475	SK-N-MC	brain:	n/a
17	chr1:78358425-78358475	K562	blood:	n/a
18	chr1:78358425-78358475	H1-hESC	embryonic stem cell:	embryo
19	chr1:78358425-78358475	HMEC	breast:	n/a
20	chr1:78358425-78358475	HNPCEpiC	eye:	n/a
21	chr1:78358425-78358475	NH-A	brain:	n/a
22	chr1:78358425-78358475	HRPEpiC	eye:	n/a
23	chr1:78358425-78358475	HEEpiC	esophagus:	n/a
24	chr1:78358425-78358475	BE2_C	brain:	n/a
25	chr1:78358425-78358475	Hepatocyte	liver:	n/a
26	chr1:78358425-78358475	MCF-7	breast:	n/a
27	chr1:78358425-78358475	GM12892	blood:	n/a
28	chr1:78358425-78358475	SK-N-SH	brain:	n/a
29	chr1:78358425-78358475	AG10803	skin:	n/a
30	chr1:78358425-78358475	ProgFib	skin:	n/a
31	chr1:78358425-78358475	U87	brain:	n/a
32	chr1:78358425-78358475	Hela-S3	cervix:	n/a
33	chr1:78358425-78358475	HEK293	kidney:	embryo
34	chr1:78358425-78358475	CMK	blood:	n/a
35	chr1:78358425-78358475	AG09319	gingival:	n/a
36	chr1:78358425-78358475	HCF	heart:	n/a
37	chr1:78358425-78358475	A549	lung:	n/a
38	chr1:78358425-78358475	GM12878	blood:	n/a
39	chr1:78358425-78358475	AoSMC	blood vessel:	n/a
40	chr1:78358425-78358475	AG09309	skin:	n/a
41	chr1:78358425-78358475	SKMC	muscle:	n/a
42	chr1:78358425-78358475	SK-N-SH_RA	brain:	n/a
43	chr1:78358425-78358475	PrEC	prostate:	n/a
44	chr1:78358425-78358475	MCF10A-Er-Src	breast:	n/a
45	chr1:78358425-78358475	HRCEpiC	kidney:	n/a
46	chr1:78358425-78358475	HCT-116	colon:	n/a
47	chr1:78358425-78358475	HL-60	blood:	n/a
48	chr1:78358425-78358475	NT2-D1	testis:	n/a
49	chr1:78358425-78358475	HIPEpiC	eye:	n/a
50	chr1:78358425-78358475	ovcar-3	ovarian:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78353975..78356210-chr1:78357586..78359985,2	K562	blood:
2	chr1:78353975..78356210-chr1:78357586..78359985,3	K562	blood:

No data

Variant related genes	Relation type
NEXN-AS1	CpG island
ENSG00000162614	Chromatin interaction
ENSG00000235927	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1325513	1.00[AFR][1000 genomes]
rs1408955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17101082	0.82[AMR][1000 genomes]
rs2032056	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2296455	0.82[AMR][1000 genomes]
rs72685315	1.00[AFR][1000 genomes]
rs72685332	0.92[EUR][1000 genomes]
rs72685333	0.92[EUR][1000 genomes]
rs72685335	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72685344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72685346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72685349	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72685355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72685362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72685366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72685370	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72685371	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72685373	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72685374	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72685376	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72685378	0.92[EUR][1000 genomes]
rs72685382	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72685386	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72685398	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72687103	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72687112	1.00[AFR][1000 genomes]
rs72687124	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1006600	chr1:78222312-78384009	Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv535011	chr1:78222312-78384009	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78352400-78359800	Active TSS	Right Ventricle	heart
2	chr1:78353200-78359200	Active TSS	Right Atrium	heart
3	chr1:78355200-78360200	Weak transcription	Lung	lung
4	chr1:78355200-78361600	Weak transcription	Pancreas	Pancrea
5	chr1:78355600-78366600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:78355800-78358800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:78355800-78359200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:78355800-78359400	Weak transcription	Brain Germinal Matrix	brain
9	chr1:78355800-78383800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:78355800-78386200	Weak transcription	Fetal Intestine Small	intestine
11	chr1:78356000-78359800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:78356000-78364200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:78356000-78365000	Weak transcription	Fetal Intestine Large	intestine
14	chr1:78356200-78359000	Weak transcription	Fetal Lung	lung
15	chr1:78356200-78366200	Weak transcription	NHDF-Ad	bronchial
16	chr1:78356200-78408600	Weak transcription	HMEC	breast
17	chr1:78356400-78358800	Weak transcription	Fetal Stomach	stomach
18	chr1:78356400-78365400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:78356400-78396000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:78356600-78365400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:78357200-78358600	Weak transcription	NHLF	lung
22	chr1:78357200-78359000	Enhancers	Fetal Heart	heart
23	chr1:78357200-78359600	Strong transcription	HSMM	muscle
24	chr1:78357200-78360200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:78357200-78360600	Strong transcription	Fetal Muscle Leg	muscle
26	chr1:78357200-78361600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:78357200-78366000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:78357400-78360000	Strong transcription	NH-A	brain
29	chr1:78357400-78365600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:78357400-78384400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:78357600-78359200	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
32	chr1:78357800-78359000	Active TSS	Left Ventricle	heart
33	chr1:78357800-78362400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:78357800-78365600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:78357800-78371000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:78358000-78358600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:78358000-78360800	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr1:78358200-78359400	Strong transcription	HSMMtube	muscle
39	chr1:78358200-78360400	Strong transcription	Osteobl	bone
40	chr1:78358200-78361600	Weak transcription	Psoas Muscle	Psoas
41	chr1:78358400-78358600	Weak transcription	Aorta	Aorta
42	chr1:78358400-78359200	Genic enhancers	Stomach Smooth Muscle	stomach
43	chr1:78358400-78362200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
44	chr1:78358400-78365800	Weak transcription	Colon Smooth Muscle	Colon

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