Variant report

Variant	rs10002045
Chromosome Location	chr4:57370566-57370567
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	POLR2A	chr4:57370473-57370787	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:57370557-57372975	K562	blood:	n/a	n/a
3	POLR2A	chr4:57370539-57370596	K562	blood:	n/a	n/a
4	POLR2A	chr4:57370237-57370614	GM12892	blood:	n/a	n/a

Variant related genes	Relation type
ARL9	TF binding region

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

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs28438730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35420817	1.00[AMR][1000 genomes]
rs56753336	1.00[AMR][1000 genomes]
rs56988045	1.00[AMR][1000 genomes]
rs57969097	1.00[AMR][1000 genomes]
rs59876036	1.00[AMR][1000 genomes]
rs60691650	1.00[AMR][1000 genomes]
rs6857233	0.81[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:126 , 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	chr4:57335800-57370800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:57336000-57371000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:57342400-57370800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr4:57342400-57371400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:57346000-57371400	Weak transcription	Pancreas	Pancrea
8	chr4:57352000-57371400	Weak transcription	Gastric	stomach
9	chr4:57352000-57371400	Weak transcription	Spleen	Spleen
10	chr4:57353800-57371400	Weak transcription	Fetal Brain Male	brain
11	chr4:57354600-57371400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr4:57356600-57371400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:57357400-57371400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr4:57357400-57371800	Weak transcription	Small Intestine	intestine
15	chr4:57357600-57371400	Weak transcription	Brain Substantia Nigra	brain
16	chr4:57357800-57371200	Weak transcription	Colonic Mucosa	Colon
17	chr4:57359200-57371200	Weak transcription	Hela-S3	cervix
18	chr4:57360400-57371200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr4:57361200-57371400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr4:57362400-57371400	Weak transcription	Aorta	Aorta
21	chr4:57362400-57371400	Weak transcription	Esophagus	oesophagus
22	chr4:57362400-57371400	Weak transcription	Right Ventricle	heart
23	chr4:57362600-57371400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr4:57362600-57371400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr4:57362800-57371400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr4:57363000-57371400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr4:57363000-57371400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr4:57363200-57371200	Weak transcription	Fetal Stomach	stomach
29	chr4:57363200-57371400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr4:57363200-57371400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:57363200-57371400	Weak transcription	Fetal Lung	lung
32	chr4:57363200-57371400	Weak transcription	Ovary	ovary
33	chr4:57363200-57371400	Weak transcription	NHLF	lung
34	chr4:57363200-57371600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:57363200-57371600	Weak transcription	Lung	lung
36	chr4:57363800-57371400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr4:57363800-57371600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:57364000-57371200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr4:57364000-57371400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:57364000-57371400	Weak transcription	Brain Angular Gyrus	brain
41	chr4:57364200-57371400	Weak transcription	Brain Germinal Matrix	brain
42	chr4:57366600-57370600	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr4:57366800-57371400	Weak transcription	Fetal Heart	heart
44	chr4:57367000-57371600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:57367800-57371400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr4:57367800-57371400	Weak transcription	HUVEC	blood vessel
47	chr4:57368000-57371000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:57368000-57371200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr4:57368000-57371400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr4:57368000-57371400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links