Variant report

Variant	rs73099642
Chromosome Location	chr5:58884826-58884827
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	TCF12	chr5:58881962-58885264	A549	lung:	n/a	n/a
2	TCF12	chr5:58884625-58885264	SK-N-SH	brain:	n/a	n/a
3	FOS	chr5:58884723-58885332	HUVEC	blood vessel:	n/a	chr5:58884983-58884994
4	FOSL2	chr5:58884759-58885222	SK-N-SH	brain:	n/a	n/a
5	RAD21	chr5:58884774-58885023	SK-N-SH_RA	brain:	n/a	n/a
6	FOSL2	chr5:58884585-58885252	A549	lung:	n/a	n/a
7	MXI1	chr5:58882578-58885137	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58883648..58886059-chr5:58910060..58912120,2	MCF-7	breast:

Variant related genes	Relation type
PDE4D	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs56841386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56966592	1.00[AFR][1000 genomes]
rs59966237	1.00[AMR][1000 genomes]
rs73099614	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73099633	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73099635	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73099639	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73099646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73099659	1.00[AFR][1000 genomes]
rs73099685	0.93[AFR][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	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58878800-58888200	Active TSS	Psoas Muscle	Psoas
2	chr5:58879200-58885000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:58883200-58885400	Enhancers	HUVEC	blood vessel
4	chr5:58883400-58885200	Enhancers	HMEC	breast
5	chr5:58883600-58885000	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr5:58883600-58885200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:58883800-58885200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:58883800-58888800	Enhancers	Hela-S3	cervix
9	chr5:58883800-58894200	Weak transcription	Aorta	Aorta
10	chr5:58884000-58885000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr5:58884000-58885000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:58884000-58885000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:58884000-58885000	Enhancers	Fetal Intestine Small	intestine
14	chr5:58884000-58885400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:58884000-58885400	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr5:58884000-58885400	Enhancers	Muscle Satellite Cultured Cells	--
17	chr5:58884000-58885400	Enhancers	HSMM	muscle
18	chr5:58884000-58887800	Weak transcription	HSMMtube	muscle
19	chr5:58884200-58885200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:58884200-58885200	Weak transcription	NH-A	brain
21	chr5:58884200-58885400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:58884200-58885400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr5:58884200-58886200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr5:58884200-58886800	Flanking Active TSS	A549	lung
25	chr5:58884200-58887000	Weak transcription	Brain Substantia Nigra	brain
26	chr5:58884200-58887200	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr5:58884200-58888000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr5:58884200-58888000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr5:58884200-58892600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr5:58884200-58892600	Weak transcription	Osteobl	bone
31	chr5:58884200-58893800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr5:58884200-58894000	Weak transcription	Right Atrium	heart
33	chr5:58884200-58894200	Weak transcription	Liver	Liver
34	chr5:58884200-58902800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr5:58884400-58885000	Enhancers	Brain Germinal Matrix	brain
36	chr5:58884400-58885000	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr5:58884400-58885200	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr5:58884400-58886200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr5:58884400-58887000	Weak transcription	Fetal Lung	lung
40	chr5:58884400-58888000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr5:58884400-58889400	Weak transcription	Brain Angular Gyrus	brain
42	chr5:58884600-58885000	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr5:58884600-58885600	Weak transcription	Stomach Mucosa	stomach
44	chr5:58884600-58885600	Enhancers	NHEK	skin
45	chr5:58884600-58886600	Weak transcription	Brain Hippocampus Middle	brain
46	chr5:58884600-58888000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr5:58884600-58888000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr5:58884600-58888000	Weak transcription	Brain Anterior Caudate	brain
49	chr5:58884600-58892200	Weak transcription	Small Intestine	intestine
50	chr5:58884600-58892600	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links