Variant report

Variant	rs3815743
Chromosome Location	chr5:7887109-7887110
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr5:7887040-7887190	GM12878	blood:	n/a	n/a
2	CTCF	chr5:7887081-7887146	K562	blood:	n/a	n/a
3	RAD21	chr5:7887083-7887622	HCT-116	colon:	n/a	chr5:7887380-7887399 chr5:7887382-7887389
4	CTCF	chr5:7887080-7887230	WI-38	lung:	n/a	n/a
5	RAD21	chr5:7886902-7887606	SK-N-SH	brain:	n/a	chr5:7887380-7887399 chr5:7887382-7887389
6	CTCF	chr5:7886927-7887602	IMR90	lung:	n/a	chr5:7887379-7887397 chr5:7887381-7887402
7	CTCF	chr5:7886960-7887110	NHLF	lung:	n/a	n/a
8	CTCF	chr5:7887073-7887127	HUVEC	blood vessel:	n/a	n/a
9	CTCF	chr5:7887040-7887190	HFF-Myc	foreskin:	n/a	n/a
10	CTCF	chr5:7887060-7887210	GM12870	blood:	n/a	n/a
11	CTCF	chr5:7886971-7887791	A549	lung:	n/a	chr5:7887379-7887397 chr5:7887381-7887402

No.	Distal block	Cell Line	Cell type
1	chr5:7866975..7869850-chr5:7885041..7887303,3	K562	blood:
2	chr5:7867651..7870301-chr5:7886397..7888680,2	MCF-7	breast:
3	chr5:7874190..7876612-chr5:7884831..7887191,2	K562	blood:
4	chr5:7873979..7876833-chr5:7886025..7888380,2	K562	blood:

Variant related genes	Relation type
MTRR	TF binding region
ENSG00000124279	Chromatin interaction
ENSG00000124275	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1078381	0.83[ASN][1000 genomes]
rs11951657	0.88[ASN][1000 genomes]
rs13163363	0.94[ASN][1000 genomes]
rs13183229	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1532268	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17245337	0.88[ASN][1000 genomes]
rs1802059	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[ASN][1000 genomes]
rs2170502	0.88[ASN][1000 genomes]
rs2892595	0.83[ASN][1000 genomes]
rs35400615	0.94[ASN][1000 genomes]
rs60014260	0.88[ASN][1000 genomes]
rs61161611	0.88[ASN][1000 genomes]
rs62342557	0.94[ASN][1000 genomes]
rs66731631	0.88[ASN][1000 genomes]
rs67030816	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67704418	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs716537	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7703296	0.88[ASN][1000 genomes]
rs7704200	0.88[ASN][1000 genomes]
rs7715062	0.88[ASN][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	nsv916892	chr5:7634377-8158890	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv949492	chr5:7682909-7953909	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv533983	chr5:7701457-8275379	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv597005	chr5:7860404-8093077	Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv427707	chr5:7866234-7966019	Strong transcription Active TSS Genic enhancers Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv525097	chr5:7887109-7896511	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7870200-7903400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:7871000-7894000	Weak transcription	Fetal Heart	heart
3	chr5:7871200-7903400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:7871200-7903600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:7871200-7903800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr5:7871400-7902400	Strong transcription	K562	blood
7	chr5:7871400-7903800	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr5:7871600-7887200	Strong transcription	Fetal Thymus	thymus
9	chr5:7871600-7887600	Strong transcription	Placenta	Placenta
10	chr5:7871600-7902800	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr5:7871600-7905000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr5:7871600-7906400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:7871600-7906800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:7871800-7907400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr5:7872000-7895200	Strong transcription	Fetal Muscle Leg	muscle
16	chr5:7872800-7887400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr5:7873200-7887600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:7873200-7903400	Strong transcription	Dnd41	blood
19	chr5:7873400-7904000	Strong transcription	Hela-S3	cervix
20	chr5:7874000-7890800	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr5:7874000-7905400	Strong transcription	Primary T cells from cord blood	blood
22	chr5:7874000-7909200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr5:7874600-7894400	Strong transcription	Adipose Nuclei	Adipose
24	chr5:7874800-7887400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr5:7874800-7887600	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr5:7875000-7906600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:7875400-7887200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:7875400-7887400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr5:7875400-7895200	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr5:7875400-7903600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr5:7875400-7903800	Strong transcription	Primary B cells from peripheral blood	blood
32	chr5:7875400-7904200	Strong transcription	Primary hematopoietic stem cells	blood
33	chr5:7875400-7904400	Strong transcription	Fetal Muscle Trunk	muscle
34	chr5:7875600-7887200	Strong transcription	Fetal Brain Female	brain
35	chr5:7875600-7904400	Strong transcription	Left Ventricle	heart
36	chr5:7878600-7911800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr5:7878800-7887400	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr5:7878800-7888600	Weak transcription	Psoas Muscle	Psoas
39	chr5:7878800-7890600	Strong transcription	NH-A	brain
40	chr5:7879000-7887200	Strong transcription	HSMM	muscle
41	chr5:7879000-7887400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr5:7879200-7887200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:7879200-7901800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:7879200-7906400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr5:7879400-7887400	Strong transcription	Osteobl	bone
46	chr5:7879400-7889800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr5:7879600-7900600	Strong transcription	Primary B cells from cord blood	blood
48	chr5:7879800-7887200	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr5:7880000-7894400	Strong transcription	Duodenum Mucosa	Duodenum
50	chr5:7880000-7903600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links