Variant report

Variant	rs2571995
Chromosome Location	chr7:99518091-99518092
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99518040-99518124	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr7:99517879-99518091	K562	blood:	n/a	n/a
3	REST	chr7:99517633-99518173	ECC-1	luminal epithelium:	n/a	n/a
4	REST	chr7:99517787-99518191	HCT-116	colon:	n/a	n/a
5	REST	chr7:99517803-99518171	HCT-116	colon:	n/a	n/a
6	SRF	chr7:99517912-99518094	HepG2	liver:	n/a	chr7:99518032-99518050 chr7:99518000-99518018
7	REST	chr7:99517761-99518118	MCF-7	breast:	n/a	n/a
8	POLR2A	chr7:99517953-99518210	HepG2	liver:	n/a	n/a
9	REST	chr7:99517678-99518160	ECC-1	luminal epithelium:	n/a	n/a
10	REST	chr7:99517748-99518117	HepG2	liver:	n/a	n/a
11	REST	chr7:99517727-99518151	HL-60	blood:	n/a	n/a
12	REST	chr7:99517726-99518101	PFSK-1	brain:	n/a	n/a
13	REST	chr7:99517775-99518205	GM12878	blood:	n/a	n/a
14	REST	chr7:99517736-99518133	K562	blood:	n/a	n/a
15	REST	chr7:99517628-99518139	PANC-1	pancreas:	n/a	n/a
16	REST	chr7:99517703-99518109	MCF-7	breast:	n/a	n/a
17	REST	chr7:99516585-99518290	HL-60	blood:	n/a	chr7:99517112-99517132
18	REST	chr7:99517777-99518114	PFSK-1	brain:	n/a	n/a
19	REST	chr7:99516778-99518193	A549	lung:	n/a	chr7:99517112-99517132
20	REST	chr7:99517732-99518120	SK-N-SH	brain:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99515720..99519605-chr7:99715122..99717935,4	K562	blood:
2	chr7:99215348..99218327-chr7:99515747..99519754,4	MCF-7	breast:
3	chr7:99516941..99519594-chr7:99565743..99568567,2	MCF-7	breast:
4	chr7:99213654..99215429-chr7:99516302..99518491,2	MCF-7	breast:
5	chr7:99516539..99518815-chr7:99613011..99615072,3	K562	blood:
6	chr7:99515746..99518740-chr7:100026570..100028641,2	MCF-7	breast:
7	chr7:99515716..99518824-chr7:99610446..99615072,4	K562	blood:
8	chr7:99515753..99518653-chr7:100025054..100026663,2	K562	blood:
9	chr7:99516652..99519200-chr7:99698709..99701368,2	MCF-7	breast:
10	chr7:99465689..99467966-chr7:99515431..99519422,3	K562	blood:
11	chr7:99516652..99519879-chr7:99696878..99699951,3	MCF-7	breast:
12	chr7:99516373..99518642-chr7:99525768..99528008,3	MCF-7	breast:
13	chr7:99415648..99420194-chr7:99515880..99518686,4	MCF-7	breast:

No data

Variant related genes	Relation type
TRIM4	TF binding region
ENSG00000106290	Chromatin interaction
ENSG00000176402	Chromatin interaction
ENSG00000221838	Chromatin interaction
ENSG00000197037	Chromatin interaction
ENSG00000166508	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000166997	Chromatin interaction
ENSG00000261511	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000106261	Chromatin interaction
ENSG00000237640	Chromatin interaction
ENSG00000260445	Chromatin interaction
ENSG00000160862	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10235630	0.86[EUR][1000 genomes]
rs1048705	0.93[ASN][1000 genomes]
rs10808114	0.96[ASN][1000 genomes]
rs1121592	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13310903	0.81[ASN][1000 genomes]
rs1865472	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099445	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2099446	0.86[EUR][1000 genomes]
rs2247761	0.96[ASN][1000 genomes]
rs2247762	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527881	0.86[EUR][1000 genomes]
rs2527899	0.97[ASN][1000 genomes]
rs2527900	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527901	0.97[ASN][1000 genomes]
rs2527902	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527903	0.97[ASN][1000 genomes]
rs2527904	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527906	0.97[ASN][1000 genomes]
rs2527908	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527909	0.97[ASN][1000 genomes]
rs2527911	0.96[ASN][1000 genomes]
rs2527912	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527913	0.96[ASN][1000 genomes]
rs2527914	0.96[ASN][1000 genomes]
rs2527915	0.96[ASN][1000 genomes]
rs2527916	0.97[ASN][1000 genomes]
rs2527918	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527919	0.96[ASN][1000 genomes]
rs2527920	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2527921	0.96[ASN][1000 genomes]
rs2527922	0.96[ASN][1000 genomes]
rs2527926	0.91[ASN][1000 genomes]
rs2527927	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2571991	0.91[ASN][1000 genomes]
rs2571992	0.97[ASN][1000 genomes]
rs2571993	0.97[ASN][1000 genomes]
rs2571994	0.97[ASN][1000 genomes]
rs2571996	0.97[ASN][1000 genomes]
rs2571997	0.97[ASN][1000 genomes]
rs2571998	0.97[ASN][1000 genomes]
rs2571999	0.96[ASN][1000 genomes]
rs2572000	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2572002	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2572003	0.96[ASN][1000 genomes]
rs2572005	0.96[ASN][1000 genomes]
rs2572006	0.96[ASN][1000 genomes]
rs2572008	0.94[ASN][1000 genomes]
rs2572009	0.94[ASN][1000 genomes]
rs2572010	0.94[ASN][1000 genomes]
rs2572011	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2572012	0.91[ASN][1000 genomes]
rs2572013	0.90[ASN][1000 genomes]
rs4727439	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7781442	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7809747	0.97[ASN][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	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2571995	TRIM4	cis	multi-tissue	Pritchard
rs2571995	TRIM4	Cis_1M	lymphoblastoid	RTeQTL
rs2571995	TRIM4	cis	Thyroid	GTEx
rs2571995	TRIM4	cis	Adipose Subcutaneous	GTEx
rs2571995	TRIM4	cis	Artery Tibial	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99515800-99518400	Active TSS	NHLF	lung
2	chr7:99516000-99518200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr7:99516000-99518200	Active TSS	Fetal Lung	lung
4	chr7:99516000-99518200	Active TSS	HSMMtube	muscle
5	chr7:99516000-99518600	Active TSS	A549	lung
6	chr7:99516200-99518200	Active TSS	Stomach Smooth Muscle	stomach
7	chr7:99516600-99518200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr7:99517200-99518200	Flanking Active TSS	Fetal Brain Male	brain
9	chr7:99517400-99518200	Flanking Active TSS	Primary T cells from cord blood	blood
10	chr7:99517400-99518200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr7:99517400-99518200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr7:99517400-99518200	Flanking Active TSS	Stomach Mucosa	stomach
13	chr7:99517400-99518400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:99517400-99518400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr7:99517400-99519400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
16	chr7:99517600-99518200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:99517600-99518200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr7:99517600-99518200	Flanking Active TSS	Brain Angular Gyrus	brain
19	chr7:99517600-99518200	Flanking Active TSS	Brain Cingulate Gyrus	brain
20	chr7:99517600-99518200	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr7:99517600-99518200	Flanking Active TSS	Brain Substantia Nigra	brain
22	chr7:99517600-99518200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr7:99517600-99518200	Enhancers	Pancreas	Pancrea
24	chr7:99517600-99518200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr7:99517600-99518200	Flanking Active TSS	Rectal Smooth Muscle	rectum
26	chr7:99517600-99518200	Enhancers	Spleen	Spleen
27	chr7:99517600-99518200	Flanking Active TSS	NHEK	skin
28	chr7:99517600-99518600	Flanking Active TSS	Dnd41	blood
29	chr7:99517600-99519400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
30	chr7:99517600-99520000	Weak transcription	Aorta	Aorta
31	chr7:99517600-99524400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr7:99517600-99526800	Weak transcription	Gastric	stomach
33	chr7:99517800-99518200	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr7:99517800-99518200	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr7:99517800-99518200	Enhancers	Primary B cells from peripheral blood	blood
36	chr7:99517800-99518200	Enhancers	Primary T cells fromperipheralblood	blood
37	chr7:99517800-99518200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr7:99517800-99518200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr7:99517800-99518200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr7:99517800-99518200	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr7:99517800-99518200	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr7:99517800-99518200	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr7:99517800-99518200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr7:99517800-99518200	Enhancers	Fetal Intestine Large	intestine
45	chr7:99517800-99518200	Enhancers	Left Ventricle	heart
46	chr7:99517800-99518200	Enhancers	Lung	lung
47	chr7:99517800-99518200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr7:99517800-99518200	Enhancers	Small Intestine	intestine
49	chr7:99517800-99518200	Flanking Active TSS	HepG2	liver
50	chr7:99517800-99518200	Flanking Active TSS	HMEC	breast

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