Variant report

Variant	rs5744150
Chromosome Location	chr1:223307808-223307809
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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223301112..223303740-chr1:223305337..223308068,3	MCF-7	breast:
2	chr1:223305860..223308306-chr1:223535536..223539484,5	MCF-7	breast:
3	chr1:223306168..223308719-chr1:223316086..223318176,3	MCF-7	breast:
4	chr1:223306279..223308015-chr1:223870177..223873121,2	MCF-7	breast:
5	chr1:223305679..223307985-chr1:223321092..223323680,2	K562	blood:
6	chr1:223305214..223307965-chr1:223314380..223316751,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SUSD4-2	chr1:223307774-223307824	NONHSAT009730

No data

Variant related genes	Relation type
ENSG00000143502	Chromatin interaction
ENSG00000187554	Chromatin interaction
ENSG00000236846	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1341985	0.90[EUR][1000 genomes]
rs1418143	0.90[EUR][1000 genomes]
rs1418144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34088950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5744104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5744106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5744107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5744144	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5744151	1.00[ASN][1000 genomes]
rs5744156	1.00[EUR][1000 genomes]
rs72743840	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72743847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72743860	0.90[EUR][1000 genomes]
rs72743869	0.90[EUR][1000 genomes]
rs72743871	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72743874	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72748469	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72748471	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72748472	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72748475	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72748482	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs988779	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1014896	chr1:223070446-223327185	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv832659	chr1:223294767-223438487	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223303200-223314600	Weak transcription	Spleen	Spleen
2	chr1:223306600-223308800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr1:223306600-223308800	Enhancers	Placenta Amnion	Placenta Amnion
4	chr1:223306600-223310000	Enhancers	Lung	lung
5	chr1:223306800-223308600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:223306800-223310000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:223306800-223310600	Enhancers	Esophagus	oesophagus
8	chr1:223307000-223308000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr1:223307000-223308400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr1:223307200-223308200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:223307400-223308000	Weak transcription	Gastric	stomach
12	chr1:223307400-223308200	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
13	chr1:223307400-223309000	Bivalent Enhancer	Fetal Thymus	thymus
14	chr1:223307600-223308000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
15	chr1:223307600-223308000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
16	chr1:223307600-223308000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
17	chr1:223307600-223308000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:223307600-223308000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr1:223307600-223308200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:223307600-223308200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
21	chr1:223307600-223308200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
22	chr1:223307600-223308200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
23	chr1:223307600-223308400	Enhancers	Fetal Intestine Large	intestine
24	chr1:223307600-223308400	Weak transcription	Ovary	ovary
25	chr1:223307600-223308400	Weak transcription	Psoas Muscle	Psoas
26	chr1:223307600-223308800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:223307600-223308800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:223307600-223308800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:223307600-223308800	Enhancers	Stomach Mucosa	stomach
30	chr1:223307600-223309200	Flanking Active TSS	NHEK	skin
31	chr1:223307600-223311400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:223307600-223311600	Enhancers	Adipose Nuclei	Adipose
33	chr1:223307600-223311600	Enhancers	Placenta	Placenta
34	chr1:223307600-223314200	Weak transcription	Right Ventricle	heart
35	chr1:223307600-223315800	Weak transcription	Right Atrium	heart
36	chr1:223307800-223308000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr1:223307800-223308000	Enhancers	Fetal Heart	heart
38	chr1:223307800-223308000	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr1:223307800-223308000	Enhancers	Stomach Smooth Muscle	stomach
40	chr1:223307800-223308200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr1:223307800-223308200	Bivalent Enhancer	Primary T cells from cord blood	blood
42	chr1:223307800-223308200	Weak transcription	Colonic Mucosa	Colon
43	chr1:223307800-223308200	Bivalent Enhancer	Fetal Kidney	kidney
44	chr1:223307800-223308200	Weak transcription	Fetal Muscle Trunk	muscle
45	chr1:223307800-223308200	Enhancers	Fetal Muscle Leg	muscle
46	chr1:223307800-223308400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr1:223307800-223308400	Bivalent Enhancer	Primary B cells from cord blood	blood
48	chr1:223307800-223308400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:223307800-223308600	Weak transcription	Aorta	Aorta
50	chr1:223307800-223308600	Enhancers	Colon Smooth Muscle	Colon

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