Variant report

Variant	rs28380685
Chromosome Location	chr4:6992971-6992972
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:6992510-6993057	K562	blood:	n/a	n/a
2	MXI1	chr4:6992776-6994296	IMR90	lung:	n/a	n/a
3	POLR2A	chr4:6992742-6995081	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr4:6992734-6992998	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:6908809..6911215-chr4:6990907..6993739,2	K562	blood:
2	chr4:6990980..6993517-chr4:7046919..7049027,2	K562	blood:
3	chr4:6782714..6785893-chr4:6989936..6993084,3	K562	blood:
4	chr4:6992471..6995105-chr4:7038359..7040025,2	MCF-7	breast:
5	chr4:6988129..6989921-chr4:6992421..6994173,2	K562	blood:
6	chr4:6909040..6912883-chr4:6987028..6993211,15	MCF-7	breast:
7	chr4:6991995..6993744-chr4:7069463..7071371,2	MCF-7	breast:

No data

Variant related genes	Relation type
TBC1D14	TF binding region
ENSG00000187904	TF binding region
ENSG00000245748	Chromatin interaction
ENSG00000109519	Chromatin interaction
ENSG00000170871	Chromatin interaction
ENSG00000132405	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10009332	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10013211	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10013696	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10015163	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10019256	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10022869	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10155208	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10937771	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12512922	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12648134	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12650200	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12650264	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13140943	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17742611	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17743234	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2301820	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2301821	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34173965	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35490604	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35772786	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3857168	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3857169	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3857170	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3857172	0.85[ASN][1000 genomes]
rs3857173	0.83[ASN][1000 genomes]
rs3892145	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3892976	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4234790	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4315786	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4484301	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4689571	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4689572	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56307635	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6834007	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7672632	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9999127	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv34033	chr4:6973270-7390621	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757919	chr4:6988148-7269901	Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv2759221	chr4:6988148-7269901	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv428436	chr4:6988148-7269901	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:6989600-6994400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr4:6989800-6994000	Enhancers	Primary T cells fromperipheralblood	blood
3	chr4:6989800-6998000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:6990000-6993000	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr4:6990000-6993200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr4:6990000-6994200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:6990000-6997400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr4:6990200-6993800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:6990200-6994400	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr4:6990200-6995200	Enhancers	Brain Substantia Nigra	brain
11	chr4:6990200-6995800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr4:6990400-6993000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr4:6990400-6993200	Enhancers	Brain Anterior Caudate	brain
14	chr4:6990400-6993200	Weak transcription	Ovary	ovary
15	chr4:6990400-6993200	Weak transcription	A549	lung
16	chr4:6990400-6993400	Weak transcription	Small Intestine	intestine
17	chr4:6990400-6993800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr4:6990400-6994200	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr4:6990400-6994200	Enhancers	Psoas Muscle	Psoas
20	chr4:6990400-6994400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr4:6990400-6994600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr4:6990400-7008800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr4:6990600-6993000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:6990600-6993000	Weak transcription	NHDF-Ad	bronchial
25	chr4:6990600-6994400	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr4:6990600-6995600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:6990800-6993200	Weak transcription	NHLF	lung
28	chr4:6991000-6994200	Genic enhancers	Fetal Muscle Leg	muscle
29	chr4:6991000-6994400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr4:6991000-6994400	Weak transcription	Fetal Kidney	kidney
31	chr4:6991000-7021800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:6991200-6993200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr4:6991200-6993200	Enhancers	Esophagus	oesophagus
34	chr4:6991200-6993200	Strong transcription	Fetal Stomach	stomach
35	chr4:6991200-6993400	Strong transcription	Fetal Intestine Small	intestine
36	chr4:6991200-6995200	Weak transcription	Placenta	Placenta
37	chr4:6991200-6995400	Enhancers	Brain Hippocampus Middle	brain
38	chr4:6991200-6995800	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr4:6991200-6996000	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr4:6991400-6993000	Weak transcription	Lung	lung
41	chr4:6991400-6993000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr4:6991400-6993000	Weak transcription	Right Atrium	heart
43	chr4:6991400-6993200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr4:6991400-6995400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr4:6991400-6996000	Weak transcription	Fetal Lung	lung
46	chr4:6991400-7000800	Weak transcription	Colonic Mucosa	Colon
47	chr4:6991600-6993000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr4:6991600-6993000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr4:6991600-6993000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr4:6991600-6993000	Weak transcription	Liver	Liver

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