Variant report

Variant	rs2301022
Chromosome Location	chr1:94372878-94372879
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:94372270..94376088-chr1:94480112..94484516,4	K562	blood:
2	chr1:94310017..94311987-chr1:94371318..94373172,2	K562	blood:
3	chr1:94344173..94346291-chr1:94372636..94375124,3	K562	blood:
4	chr1:93811453..93814121-chr1:94372637..94375148,3	K562	blood:
5	chr1:94340990..94343514-chr1:94369991..94373741,3	K562	blood:
6	chr1:94350854..94353775-chr1:94372233..94374131,2	K562	blood:
7	chr1:93811453..93813762-chr1:94372603..94376116,3	K562	blood:
8	chr1:94310017..94313015-chr1:94371318..94373997,3	K562	blood:
9	chr1:94342014..94348814-chr1:94369991..94376733,14	K562	blood:

No data

Variant related genes	Relation type
ENSG00000137936	Chromatin interaction
ENSG00000198691	Chromatin interaction
ENSG00000067334	Chromatin interaction
ENSG00000260464	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000117505	Chromatin interaction
ENSG00000223745	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1473712	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1473713	0.96[ASN][1000 genomes]
rs1884019	0.94[JPT][hapmap]
rs2064765	0.88[ASN][1000 genomes]
rs2144872	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2144873	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2747042	0.94[JPT][hapmap]
rs3789453	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789457	0.88[CEU][hapmap];0.94[JPT][hapmap]
rs4427413	0.88[ASN][1000 genomes]
rs4578232	0.86[ASN][1000 genomes]
rs4847268	0.86[ASN][1000 genomes]
rs6660210	0.94[JPT][hapmap]
rs6679978	0.93[ASN][1000 genomes]
rs6683813	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6703130	0.94[ASN][1000 genomes]
rs743110	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs743112	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7523787	0.94[JPT][hapmap]
rs7526920	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7552293	0.94[JPT][hapmap]
rs9725707	0.93[ASN][1000 genomes]
rs990576	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523355	chr1:94351328-94385591	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv3404764	chr1:94372564-94377162	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2301022	GEMIN8P4	cis	cerebellum	SCAN
rs2301022	GCLM	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94345000-94374200	Weak transcription	Gastric	stomach
2	chr1:94345000-94374200	Weak transcription	Spleen	Spleen
3	chr1:94345200-94374000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:94345200-94374200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:94345400-94373200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:94345400-94373200	Weak transcription	Brain Substantia Nigra	brain
7	chr1:94345400-94373800	Weak transcription	Fetal Stomach	stomach
8	chr1:94345400-94374000	Weak transcription	Right Ventricle	heart
9	chr1:94345600-94373000	Weak transcription	Fetal Brain Female	brain
10	chr1:94345600-94373200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:94345600-94373200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:94345600-94373200	Weak transcription	Fetal Brain Male	brain
13	chr1:94345600-94373400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:94345600-94373400	Weak transcription	Psoas Muscle	Psoas
15	chr1:94345600-94373400	Weak transcription	Stomach Mucosa	stomach
16	chr1:94345600-94373600	Weak transcription	Brain Germinal Matrix	brain
17	chr1:94347400-94374200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:94352800-94373000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:94354600-94373400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:94357200-94373800	Weak transcription	Thymus	Thymus
21	chr1:94357400-94374000	Weak transcription	Aorta	Aorta
22	chr1:94357600-94374200	Weak transcription	Pancreas	Pancrea
23	chr1:94357800-94373200	Weak transcription	Esophagus	oesophagus
24	chr1:94357800-94374000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:94359800-94373800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:94359800-94374000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr1:94360400-94373200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:94360800-94373000	Weak transcription	Fetal Heart	heart
29	chr1:94362400-94373200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:94362400-94373200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:94362400-94373200	Weak transcription	Brain Angular Gyrus	brain
32	chr1:94362600-94373200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:94362600-94373400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr1:94362600-94373800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:94362600-94374200	Weak transcription	Left Ventricle	heart
36	chr1:94362800-94373000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:94362800-94373200	Weak transcription	Fetal Muscle Leg	muscle
38	chr1:94362800-94373400	Weak transcription	Fetal Thymus	thymus
39	chr1:94362800-94374000	Weak transcription	Ovary	ovary
40	chr1:94363000-94373200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr1:94363400-94373200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:94366200-94373400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:94366800-94374000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:94367000-94373200	Weak transcription	HSMMtube	muscle
45	chr1:94367200-94373000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:94367200-94373400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:94367200-94373800	Weak transcription	Placenta	Placenta
48	chr1:94369200-94373800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:94369200-94373800	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr1:94369400-94373000	Enhancers	Duodenum Mucosa	Duodenum

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