Variant report

Variant	rs28439752
Chromosome Location	chr5:112622143-112622144
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112621858..112623508-chr5:112628584..112630784,2	K562	blood:

Variant related genes	Relation type
ENSG00000171444	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10037836	1.00[AMR][1000 genomes]
rs10037845	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10042401	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10056104	1.00[AMR][1000 genomes]
rs10477489	1.00[AMR][1000 genomes]
rs10478116	1.00[AMR][1000 genomes]
rs11958613	1.00[AMR][1000 genomes]
rs12110055	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13357188	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13358281	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17135568	0.89[AMR][1000 genomes]
rs17135570	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs28462299	1.00[AMR][1000 genomes]
rs28497391	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2860051	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28711712	1.00[AMR][1000 genomes]
rs55889115	1.00[AMR][1000 genomes]
rs57727389	0.89[AMR][1000 genomes]
rs59032550	1.00[AMR][1000 genomes]
rs61560548	1.00[AMR][1000 genomes]
rs73781507	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73781509	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73781510	1.00[AMR][1000 genomes]
rs73781511	1.00[AMR][1000 genomes]
rs73781512	1.00[AMR][1000 genomes]
rs7718459	1.00[AMR][1000 genomes]
rs7720189	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7736171	0.90[AFR][1000 genomes];1.00[AMR][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	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1024747	chr5:112592710-112679373	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1018078	chr5:112615220-112657404	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv949165	chr5:112615626-112730216	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112586600-112623600	Weak transcription	Pancreas	Pancrea
2	chr5:112608000-112628200	Weak transcription	HMEC	breast
3	chr5:112610000-112628200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:112610800-112623200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:112611000-112628200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:112612000-112623800	Weak transcription	Fetal Muscle Leg	muscle
7	chr5:112612000-112625200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:112612200-112625200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:112614200-112625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:112615000-112625200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:112616800-112623400	Weak transcription	NHEK	skin
12	chr5:112616800-112623800	Weak transcription	Esophagus	oesophagus
13	chr5:112617800-112625400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:112617800-112628600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr5:112618200-112623600	Weak transcription	Gastric	stomach
16	chr5:112618400-112628000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr5:112618400-112628200	Weak transcription	Fetal Kidney	kidney
18	chr5:112618400-112628200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr5:112618400-112628400	Weak transcription	Fetal Stomach	stomach
20	chr5:112618600-112625600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr5:112619000-112626800	Weak transcription	Liver	Liver
22	chr5:112619000-112628600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr5:112619000-112628800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr5:112619200-112625600	Weak transcription	Fetal Lung	lung
25	chr5:112619400-112624000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr5:112619400-112625200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr5:112619600-112625200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr5:112620000-112628200	Weak transcription	Brain Anterior Caudate	brain
29	chr5:112620000-112628200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr5:112620400-112625200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr5:112621000-112622400	Enhancers	Ovary	ovary
32	chr5:112621200-112622200	Enhancers	Left Ventricle	heart
33	chr5:112621200-112622200	Enhancers	Psoas Muscle	Psoas
34	chr5:112621200-112622400	Enhancers	Adipose Nuclei	Adipose
35	chr5:112621200-112622400	Enhancers	Right Atrium	heart
36	chr5:112621200-112622800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr5:112621600-112622400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:112621600-112622800	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr5:112621600-112623800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr5:112621600-112625200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr5:112621800-112622200	Weak transcription	Fetal Heart	heart
42	chr5:112621800-112622600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr5:112622000-112622200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr5:112622000-112622200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:112622000-112622200	Enhancers	Brain Angular Gyrus	brain
46	chr5:112622000-112625200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr5:112622000-112626800	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links