Variant report

Variant	rs73229007
Chromosome Location	chr5:112316920-112316921
allele	C/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	FOS	chr5:112316770-112316930	MCF10A-Er-Src	breast:	n/a	n/a
2	GATA3	chr5:112316688-112317040	T-47D	breast:	n/a	n/a
3	WRNIP1	chr5:112316731-112316954	GM12878	blood:	n/a	n/a
4	EP300	chr5:112316645-112317038	T-47D	breast:	n/a	n/a
5	GATA3	chr5:112316685-112317079	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:112311145..112314018-chr5:112314616..112318663,4	MCF-7	breast:
2	chr5:112202949..112204762-chr5:112314290..112317071,2	MCF-7	breast:
3	chr5:112312383..112314551-chr5:112314826..112319334,4	MCF-7	breast:

Variant related genes	Relation type
DCP2	TF binding region
ENSG00000172795	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs17135245	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59624235	1.00[AMR][1000 genomes]
rs6883462	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs726038	1.00[AMR][1000 genomes]
rs73221991	1.00[AMR][1000 genomes]
rs73223916	1.00[AMR][1000 genomes]
rs73227402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73235110	1.00[AMR][1000 genomes]
rs73235120	1.00[AMR][1000 genomes]
rs73235125	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	nsv1028759	chr5:112300490-112358514	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112313200-112329000	Weak transcription	Spleen	Spleen
2	chr5:112313800-112337600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:112314000-112317600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:112314000-112317800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:112314000-112318800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:112314000-112320000	Weak transcription	Pancreas	Pancrea
7	chr5:112314000-112329000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:112314000-112335400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:112314000-112337200	Weak transcription	Lung	lung
10	chr5:112314000-112338200	Weak transcription	Gastric	stomach
11	chr5:112314200-112317000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr5:112314200-112317600	Weak transcription	Right Ventricle	heart
13	chr5:112314200-112318000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:112314200-112319800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr5:112314200-112326800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:112314200-112328800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr5:112314200-112328800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr5:112314200-112332000	Weak transcription	Fetal Kidney	kidney
19	chr5:112314200-112332000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:112314200-112337000	Weak transcription	HSMMtube	muscle
21	chr5:112314200-112338200	Weak transcription	Aorta	Aorta
22	chr5:112314200-112341000	Weak transcription	Small Intestine	intestine
23	chr5:112314200-112349600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr5:112314200-112356800	Weak transcription	Stomach Mucosa	stomach
25	chr5:112314200-112362600	Weak transcription	Colonic Mucosa	Colon
26	chr5:112314400-112317400	Weak transcription	Fetal Intestine Small	intestine
27	chr5:112314400-112317400	Weak transcription	Fetal Stomach	stomach
28	chr5:112314400-112318200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr5:112314400-112322400	Weak transcription	Thymus	Thymus
30	chr5:112314400-112338400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr5:112314800-112317400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr5:112314800-112318200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr5:112314800-112318200	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr5:112314800-112320000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr5:112314800-112322400	Weak transcription	Liver	Liver
36	chr5:112314800-112324400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr5:112314800-112324400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr5:112314800-112325800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr5:112314800-112332000	Weak transcription	Brain Hippocampus Middle	brain
40	chr5:112314800-112332000	Weak transcription	NHLF	lung
41	chr5:112314800-112332200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:112314800-112337200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr5:112314800-112349200	Weak transcription	Brain Substantia Nigra	brain
44	chr5:112315400-112330800	Weak transcription	Brain Anterior Caudate	brain
45	chr5:112315600-112317200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr5:112315600-112317400	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr5:112315600-112317400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr5:112315600-112317800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr5:112315600-112318200	Enhancers	HepG2	liver
50	chr5:112315600-112318600	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links