Variant report

Variant	rs28503748
Chromosome Location	chr4:57369914-57369915
allele	G/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	POLR2A	chr4:57369753-57370182	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ARL9	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10001639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10003484	1.00[AMR][1000 genomes]
rs10015839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10016054	1.00[AMR][1000 genomes]
rs10018091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10018803	1.00[AMR][1000 genomes]
rs10020554	1.00[AMR][1000 genomes]
rs10222713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13434512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28398277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28401187	1.00[AMR][1000 genomes]
rs28552845	1.00[AMR][1000 genomes]
rs28571922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28653752	1.00[AMR][1000 genomes]
rs28891686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9993594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9994079	1.00[AMR][1000 genomes]
rs9994122	1.00[AFR][1000 genomes];1.00[AMR][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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv829941	chr4:57359551-57553136	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 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	chr4:57334800-57371200	Weak transcription	Stomach Mucosa	stomach
2	chr4:57335200-57371400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:57335600-57370200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr4:57335800-57370200	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr4:57335800-57370800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:57336000-57370000	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr4:57336000-57370000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr4:57336000-57370200	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr4:57336000-57371000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:57336200-57370000	Strong transcription	Placenta	Placenta
11	chr4:57336200-57370400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:57336400-57370200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:57342000-57370200	Strong transcription	Primary B cells from peripheral blood	blood
14	chr4:57342400-57370800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr4:57342400-57371400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr4:57346000-57371400	Weak transcription	Pancreas	Pancrea
17	chr4:57352000-57371400	Weak transcription	Gastric	stomach
18	chr4:57352000-57371400	Weak transcription	Spleen	Spleen
19	chr4:57353800-57371400	Weak transcription	Fetal Brain Male	brain
20	chr4:57354600-57371400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr4:57356600-57371400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:57357400-57371400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr4:57357400-57371800	Weak transcription	Small Intestine	intestine
24	chr4:57357600-57371400	Weak transcription	Brain Substantia Nigra	brain
25	chr4:57357800-57371200	Weak transcription	Colonic Mucosa	Colon
26	chr4:57359200-57371200	Weak transcription	Hela-S3	cervix
27	chr4:57360400-57371200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr4:57361200-57371400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr4:57362400-57371400	Weak transcription	Aorta	Aorta
30	chr4:57362400-57371400	Weak transcription	Esophagus	oesophagus
31	chr4:57362400-57371400	Weak transcription	Right Ventricle	heart
32	chr4:57362600-57371400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr4:57362600-57371400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr4:57362800-57371400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr4:57363000-57371400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr4:57363000-57371400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr4:57363200-57371200	Weak transcription	Fetal Stomach	stomach
38	chr4:57363200-57371400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr4:57363200-57371400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:57363200-57371400	Weak transcription	Fetal Lung	lung
41	chr4:57363200-57371400	Weak transcription	Ovary	ovary
42	chr4:57363200-57371400	Weak transcription	NHLF	lung
43	chr4:57363200-57371600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:57363200-57371600	Weak transcription	Lung	lung
45	chr4:57363800-57371400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr4:57363800-57371600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr4:57364000-57371200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr4:57364000-57371400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr4:57364000-57371400	Weak transcription	Brain Angular Gyrus	brain
50	chr4:57364200-57371400	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links