Variant report

Variant	rs10020554
Chromosome Location	chr4:57366982-57366983
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	chr4:57366592-57367003	GM12892	blood:	n/a	n/a
2	POLR2A	chr4:57366498-57367055	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:57333730..57336121-chr4:57366931..57369168,2	K562	blood:
2	chr4:57363740..57365752-chr4:57366897..57368422,2	K562	blood:
3	chr4:57334621..57337468-chr4:57366931..57368856,2	K562	blood:

Variant related genes	Relation type
ARL9	TF binding region
ENSG00000174780	Chromatin interaction

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[AMR][1000 genomes]
rs10003484	1.00[AMR][1000 genomes]
rs10015839	1.00[AMR][1000 genomes]
rs10016054	1.00[AMR][1000 genomes]
rs10018091	1.00[AMR][1000 genomes]
rs10018803	1.00[AMR][1000 genomes]
rs10222713	1.00[AMR][1000 genomes]
rs13434512	1.00[AMR][1000 genomes]
rs28398277	1.00[AMR][1000 genomes]
rs28401187	1.00[AMR][1000 genomes]
rs28503748	1.00[AMR][1000 genomes]
rs28552845	1.00[AMR][1000 genomes]
rs28571922	1.00[AMR][1000 genomes]
rs28653752	1.00[AMR][1000 genomes]
rs28891686	1.00[AMR][1000 genomes]
rs9993594	1.00[AMR][1000 genomes]
rs9994079	1.00[AMR][1000 genomes]
rs9994122	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	chr4:57335800-57369200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:57335800-57370200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr4:57335800-57370800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:57336000-57369400	Strong transcription	Liver	Liver
8	chr4:57336000-57369800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:57336000-57370000	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr4:57336000-57370000	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr4:57336000-57370200	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:57336000-57371000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:57336200-57369200	Strong transcription	Fetal Thymus	thymus
14	chr4:57336200-57370000	Strong transcription	Placenta	Placenta
15	chr4:57336200-57370400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:57336400-57368200	Strong transcription	Fetal Muscle Trunk	muscle
17	chr4:57336400-57369200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:57336400-57369200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:57336400-57370200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:57336600-57369200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr4:57337200-57369200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:57337800-57369200	Strong transcription	Adipose Nuclei	Adipose
23	chr4:57337800-57369400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:57340800-57369000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr4:57342000-57370200	Strong transcription	Primary B cells from peripheral blood	blood
26	chr4:57342400-57370800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr4:57342400-57371400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr4:57346000-57371400	Weak transcription	Pancreas	Pancrea
29	chr4:57352000-57371400	Weak transcription	Gastric	stomach
30	chr4:57352000-57371400	Weak transcription	Spleen	Spleen
31	chr4:57353800-57371400	Weak transcription	Fetal Brain Male	brain
32	chr4:57354600-57371400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr4:57355400-57369800	Weak transcription	Psoas Muscle	Psoas
34	chr4:57356600-57371400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr4:57357200-57368800	Weak transcription	Fetal Kidney	kidney
36	chr4:57357400-57371400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr4:57357400-57371800	Weak transcription	Small Intestine	intestine
38	chr4:57357600-57371400	Weak transcription	Brain Substantia Nigra	brain
39	chr4:57357800-57371200	Weak transcription	Colonic Mucosa	Colon
40	chr4:57358800-57368200	Weak transcription	Colon Smooth Muscle	Colon
41	chr4:57359200-57371200	Weak transcription	Hela-S3	cervix
42	chr4:57360000-57368400	Strong transcription	Left Ventricle	heart
43	chr4:57360400-57371200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr4:57360800-57367400	Weak transcription	Thymus	Thymus
45	chr4:57361200-57371400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr4:57362400-57367600	Weak transcription	Primary B cells from cord blood	blood
47	chr4:57362400-57371400	Weak transcription	Aorta	Aorta
48	chr4:57362400-57371400	Weak transcription	Esophagus	oesophagus
49	chr4:57362400-57371400	Weak transcription	Right Ventricle	heart
50	chr4:57362600-57367600	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links