Variant report

Variant	rs3820653
Chromosome Location	chr1:173021222-173021223
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:0)
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	chr1:173021195-173021245	AG10803	skin:	n/a
2	chr1:173021195-173021245	GM12878	blood:	n/a
3	chr1:173021195-173021245	GM19239	blood:	n/a
4	chr1:173021195-173021245	SK-N-SH_RA	brain:	n/a
5	chr1:173021195-173021245	Hepatocyte	liver:	n/a
6	chr1:173021195-173021245	AG09319	gingival:	n/a
7	chr1:173021195-173021245	NHBE	bronchial:	n/a
8	chr1:173021195-173021245	HCPEpiC	choroid plexus:	n/a
9	chr1:173021195-173021245	K562	blood:	n/a
10	chr1:173021195-173021245	NH-A	brain:	n/a
11	chr1:173021195-173021245	BJ	skin:	n/a
12	chr1:173021195-173021245	HL-60	blood:	n/a
13	chr1:173021195-173021245	HRCEpiC	kidney:	n/a
14	chr1:173021195-173021245	AG09309	skin:	n/a
15	chr1:173021195-173021245	U87	brain:	n/a
16	chr1:173021195-173021245	PFSK-1	brain:	n/a
17	chr1:173021195-173021245	MCF10A-Er-Src	breast:	n/a
18	chr1:173021195-173021245	CMK	blood:	n/a
19	chr1:173021195-173021245	HAEpiC	amniotic membrane:	n/a
20	chr1:173021195-173021245	RPTEC	kidney:	n/a
21	chr1:173021195-173021245	IMR90	lung:	fetal
22	chr1:173021195-173021245	Jurkat	blood:	n/a
23	chr1:173021195-173021245	HUVEC	blood vessel:	n/a
24	chr1:173021195-173021245	BE2_C	brain:	n/a
25	chr1:173021195-173021245	SAEC	small airway:	n/a
26	chr1:173021195-173021245	GM12892	blood:	n/a
27	chr1:173021195-173021245	HEK293	kidney:	embryo
28	chr1:173021195-173021245	HRE	kidney:	n/a
29	chr1:173021195-173021245	ovcar-3	ovarian:	n/a
30	chr1:173021195-173021245	MCF-7	breast:	n/a
31	chr1:173021195-173021245	Caco-2	colon:	n/a
32	chr1:173021195-173021245	GM06990	blood:	n/a
33	chr1:173021195-173021245	ECC-1	luminal epithelium:	n/a
34	chr1:173021195-173021245	AG04449	skin:	fetal
35	chr1:173021195-173021245	HCF	heart:	n/a
36	chr1:173021195-173021245	PANC-1	pancreas:	n/a
37	chr1:173021195-173021245	HCT-116	colon:	n/a
38	chr1:173021195-173021245	NHDF-neo	bronchial:	n/a
39	chr1:173021195-173021245	HNPCEpiC	eye:	n/a
40	chr1:173021195-173021245	LNCaP	prostate:	n/a
41	chr1:173021195-173021245	HPAEpiC	pulmonary alveolar:	n/a
42	chr1:173021195-173021245	NB4	blood:	n/a
43	chr1:173021195-173021245	PrEC	prostate:	n/a
44	chr1:173021195-173021245	AG04450	lung:	fetal
45	chr1:173021195-173021245	SK-N-SH	brain:	n/a
46	chr1:173021195-173021245	SK-N-MC	brain:	n/a
47	chr1:173021195-173021245	AoSMC	blood vessel:	n/a
48	chr1:173021195-173021245	HEEpiC	esophagus:	n/a
49	chr1:173021195-173021245	HMEC	breast:	n/a
50	chr1:173021195-173021245	HIPEpiC	eye:	n/a

No data

Variant related genes	Relation type
TNFSF18	CpG island

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10489271	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12401349	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12405785	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12406059	1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16828402	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16845400	0.87[ASN][1000 genomes]
rs16845403	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16845438	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16845442	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2207057	0.95[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2207059	0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2422273	0.95[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4916206	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4916298	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4916303	0.87[ASN][1000 genomes]
rs4916305	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs714991	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831904	chr1:172912110-173070429	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv533953	chr1:172939335-173133255	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173018400-173021600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:173019600-173021600	Enhancers	NHEK	skin
3	chr1:173019600-173022200	Enhancers	Duodenum Smooth Muscle	Duodenum
4	chr1:173019600-173022600	Enhancers	HMEC	breast
5	chr1:173019800-173021800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:173019800-173022000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:173019800-173022600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr1:173019800-173022600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:173019800-173022600	Enhancers	Hela-S3	cervix
10	chr1:173020000-173022400	Enhancers	Liver	Liver
11	chr1:173020000-173022600	Enhancers	Stomach Mucosa	stomach
12	chr1:173020000-173023200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:173020200-173021400	Weak transcription	A549	lung
14	chr1:173020200-173022200	Enhancers	Adipose Nuclei	Adipose
15	chr1:173020200-173022200	Enhancers	Fetal Lung	lung
16	chr1:173020400-173021400	Weak transcription	Colon Smooth Muscle	Colon
17	chr1:173020400-173021400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:173020600-173021800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:173020600-173021800	Weak transcription	NH-A	brain
20	chr1:173020600-173022000	Weak transcription	HSMM	muscle
21	chr1:173020600-173022400	Enhancers	HUVEC	blood vessel
22	chr1:173020800-173021800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr1:173020800-173022000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr1:173021000-173021800	Enhancers	Fetal Kidney	kidney
25	chr1:173021000-173024000	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr1:173021000-173024000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr1:173021200-173021800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:173021200-173022000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:173021200-173022000	Weak transcription	NHLF	lung

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