Variant report

Variant	rs72671982
Chromosome Location	chr1:45142076-45142077
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr1:45142066-45143303	HCT-116	colon:	n/a	n/a
2	ATF2	chr1:45141982-45142640	GM12878	blood:	n/a	n/a
3	BCLAF1	chr1:45141982-45143243	GM12878	blood:	n/a	n/a
4	RCOR1	chr1:45141816-45143125	IMR90	lung:	n/a	n/a
5	MTA3	chr1:45141604-45143332	GM12878	blood:	n/a	n/a
6	PML	chr1:45141971-45143233	GM12878	blood:	n/a	n/a
7	STAT3	chr1:45142074-45142445	MCF10A-Er-Src	breast:	n/a	n/a
8	FOXM1	chr1:45142074-45143262	GM12878	blood:	n/a	n/a
9	SPI1	chr1:45141817-45142712	GM12878	blood:	n/a	n/a
10	TEAD4	chr1:45142044-45143234	K562	blood:	n/a	n/a
11	RUNX3	chr1:45142052-45143231	GM12878	blood:	n/a	n/a
12	FOS	chr1:45141962-45142499	HUVEC	blood vessel:	n/a	n/a
13	NR2F2	chr1:45142004-45142677	K562	blood:	n/a	n/a
14	POLR2A	chr1:45142026-45142541	HCT-116	colon:	n/a	n/a
15	IKZF1	chr1:45141795-45143127	GM12878	blood:	n/a	n/a
16	NFIC	chr1:45141946-45143245	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:45142024-45142543	HUVEC	blood vessel:	n/a	n/a
18	RUNX3	chr1:45142057-45143190	GM12878	blood:	n/a	n/a
19	CTCF	chr1:45141940-45142090	HCPEpiC	choroid plexus:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45100964..45102855-chr1:45141535..45143464,3	K562	blood:
2	chr1:45140788..45143214-chr1:45143227..45145914,3	K562	blood:
3	chr1:45138628..45142139-chr1:45284311..45287293,3	K562	blood:
4	chr1:45095169..45100377-chr1:45133934..45142864,15	K562	blood:
5	chr1:45141360..45143507-chr1:45193675..45195240,2	MCF-7	breast:
6	chr1:45140169..45143277-chr1:45195258..45198293,3	MCF-7	breast:
7	chr1:45141963..45146217-chr1:45184774..45188907,4	MCF-7	breast:
8	chr1:45105542..45109261-chr1:45139821..45142236,3	K562	blood:

No data

Variant related genes	Relation type
TMEM53	TF binding region
ENSG00000200169	Chromatin interaction
ENSG00000187147	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000199377	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12036630	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1321703	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16832186	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16832188	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3738733	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3754421	0.90[EUR][1000 genomes]
rs3768438	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3768441	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3850854	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3889695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41524944	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4660286	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4660814	0.90[EUR][1000 genomes]
rs4660819	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660820	0.90[AMR][1000 genomes]
rs56756630	0.90[EUR][1000 genomes]
rs59834392	0.90[EUR][1000 genomes]
rs66509359	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671943	0.90[EUR][1000 genomes]
rs72671944	0.90[EUR][1000 genomes]
rs72671945	0.90[EUR][1000 genomes]
rs72671948	0.90[EUR][1000 genomes]
rs72671950	0.90[EUR][1000 genomes]
rs72671962	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671966	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671967	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671971	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671974	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72671984	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72671988	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7532001	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7539607	1.00[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	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
5	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
6	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45140400-45143400	Enhancers	Small Intestine	intestine
2	chr1:45140600-45142200	Enhancers	Spleen	Spleen
3	chr1:45140600-45142600	Weak transcription	Gastric	stomach
4	chr1:45140600-45150200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:45140800-45142200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:45140800-45142600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:45140800-45143000	Enhancers	Primary B cells from peripheral blood	blood
8	chr1:45140800-45143000	Enhancers	Placenta	Placenta
9	chr1:45140800-45143000	Enhancers	Fetal Thymus	thymus
10	chr1:45140800-45143000	Enhancers	HUVEC	blood vessel
11	chr1:45140800-45143600	Enhancers	Fetal Intestine Large	intestine
12	chr1:45140800-45143600	Enhancers	Stomach Mucosa	stomach
13	chr1:45140800-45143800	Enhancers	Colonic Mucosa	Colon
14	chr1:45140800-45144000	Enhancers	Primary B cells from cord blood	blood
15	chr1:45140800-45145000	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr1:45140800-45146800	Weak transcription	Esophagus	oesophagus
17	chr1:45141000-45142200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:45141000-45142200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:45141000-45142200	Weak transcription	Fetal Heart	heart
20	chr1:45141000-45142400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:45141000-45142400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:45141000-45142400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:45141000-45142400	Enhancers	HSMMtube	muscle
24	chr1:45141000-45142600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:45141000-45142600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:45141000-45142600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:45141000-45143000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:45141000-45143400	Enhancers	Fetal Intestine Small	intestine
29	chr1:45141000-45143600	Enhancers	NHDF-Ad	bronchial
30	chr1:45141000-45143800	Enhancers	Primary hematopoietic stem cells	blood
31	chr1:45141000-45143800	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr1:45141000-45144000	Enhancers	Duodenum Mucosa	Duodenum
33	chr1:45141000-45144400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:45141000-45144800	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr1:45141000-45144800	Enhancers	Liver	Liver
36	chr1:45141000-45144800	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr1:45141000-45145000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:45141000-45145200	Enhancers	Adipose Nuclei	Adipose
39	chr1:45141000-45146000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:45141000-45147000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:45141000-45147400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr1:45141000-45154200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr1:45141000-45154800	Weak transcription	Ovary	ovary
44	chr1:45141200-45142200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:45141200-45142800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:45141200-45142800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:45141200-45142800	Weak transcription	Brain Substantia Nigra	brain
48	chr1:45141200-45143000	Weak transcription	Fetal Stomach	stomach
49	chr1:45141200-45143000	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr1:45141200-45143400	Enhancers	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links