Variant report

Variant	rs3962814
Chromosome Location	chr5:112260084-112260085
allele	C/T
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	RUNX3	chr5:112259085-112260109	GM12878	blood:	n/a	n/a
2	RUNX3	chr5:112258815-112260088	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:112255914..112262078-chr5:112308752..112315375,16	MCF-7	breast:
2	chr5:112196028..112199860-chr5:112256680..112260462,5	MCF-7	breast:
3	chr5:112195239..112200315-chr5:112255126..112261929,8	MCF-7	breast:
4	chr5:112258754..112260468-chr5:112260829..112262760,2	MCF-7	breast:

Variant related genes	Relation type
REEP5	TF binding region
ENSG00000172795	Chromatin interaction
ENSG00000153037	Chromatin interaction
ENSG00000272869	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10064080	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10515450	0.88[EUR][1000 genomes]
rs12188113	0.94[EUR][1000 genomes]
rs13354064	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13360667	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17135193	0.88[ASN][1000 genomes]
rs17553240	0.93[EUR][1000 genomes]
rs1833560	0.83[ASN][1000 genomes]
rs28635838	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28789211	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4145650	0.96[EUR][1000 genomes]
rs56364425	0.96[EUR][1000 genomes]
rs57749964	0.83[ASN][1000 genomes]
rs58775131	0.81[ASN][1000 genomes]
rs59349522	0.88[ASN][1000 genomes]
rs6864647	0.86[ASN][1000 genomes]
rs728347	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73227370	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73227382	0.83[ASN][1000 genomes]
rs73789251	0.91[EUR][1000 genomes]
rs73789266	0.96[EUR][1000 genomes]
rs7730241	0.81[ASN][1000 genomes]
rs7730441	0.81[ASN][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	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv529536	chr5:112174106-112269758	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1019756	chr5:112242315-112325943	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	esv2763866	chr5:112254282-112284223	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112258000-112265000	Weak transcription	Small Intestine	intestine
2	chr5:112258200-112260400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr5:112258200-112260600	Flanking Active TSS	GM12878-XiMat	blood
4	chr5:112258400-112260800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:112258400-112287400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:112258600-112264000	Weak transcription	A549	lung
7	chr5:112258600-112264200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:112258800-112263600	Weak transcription	Fetal Intestine Small	intestine
9	chr5:112259000-112263400	Weak transcription	Hela-S3	cervix
10	chr5:112259000-112267200	Weak transcription	Psoas Muscle	Psoas
11	chr5:112259000-112267200	Weak transcription	Right Atrium	heart
12	chr5:112259000-112269200	Weak transcription	Osteobl	bone
13	chr5:112259200-112260600	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr5:112259200-112262000	Weak transcription	Fetal Brain Male	brain
15	chr5:112259400-112260200	Enhancers	Primary T cells fromperipheralblood	blood
16	chr5:112259400-112260200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr5:112259400-112260400	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr5:112259400-112260400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr5:112259400-112260400	Enhancers	K562	blood
20	chr5:112259400-112261400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr5:112259400-112261600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr5:112259400-112264000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr5:112259600-112260200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr5:112259600-112260200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr5:112259600-112260200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:112259600-112260600	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr5:112259600-112260600	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr5:112259600-112261600	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr5:112259600-112265000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr5:112259600-112267600	Enhancers	Primary B cells from peripheral blood	blood
31	chr5:112259800-112260200	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr5:112259800-112262600	Weak transcription	Primary T cells from cord blood	blood
33	chr5:112259800-112262600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr5:112259800-112263000	Weak transcription	Placenta	Placenta
35	chr5:112259800-112265200	Enhancers	Primary B cells from cord blood	blood
36	chr5:112260000-112261200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr5:112260000-112261400	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr5:112260000-112262600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr5:112260000-112262800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr5:112260000-112263000	Weak transcription	Fetal Thymus	thymus
41	chr5:112260000-112263200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr5:112260000-112263200	Weak transcription	Dnd41	blood

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