Variant report

Variant	rs2121558
Chromosome Location	chr4:106552733-106552734
allele	A/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	CHD1	chr4:106552570-106552744	GM12878	blood:	n/a	n/a
2	WRNIP1	chr4:106552586-106552744	GM12878	blood:	n/a	n/a
3	FOS	chr4:106552569-106552856	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr4:106552523-106552853	MCF10A-Er-Src	breast:	n/a	n/a
5	RUNX3	chr4:106552387-106552888	GM12878	blood:	n/a	n/a
6	ZNF143	chr4:106552661-106552805	GM12878	blood:	n/a	n/a
7	NFIC	chr4:106552353-106553121	GM12878	blood:	n/a	n/a
8	STAT3	chr4:106552567-106553078	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr4:106552638-106552772	MCF10A-Er-Src	breast:	n/a	n/a
10	FOXM1	chr4:106552454-106552926	GM12878	blood:	n/a	n/a
11	EBF1	chr4:106552478-106552766	GM12878	blood:	n/a	n/a
12	EP300	chr4:106552553-106552753	GM12878	blood:	n/a	n/a
13	FOS	chr4:106552517-106552821	MCF10A-Er-Src	breast:	n/a	n/a
14	MYC	chr4:106552427-106552777	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106551066..106553304-chr4:106554764..106557065,2	K562	blood:

Variant related genes	Relation type
ARHGEF38	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10025790	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10032142	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10032283	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10034172	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097895	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11726715	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13138544	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1447093	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1447094	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1447098	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1447099	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1447100	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1447101	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17036041	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17036049	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2044536	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28415919	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3822277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4484305	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67822595	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7686722	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7699846	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs921113	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9999133	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9999326	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106516000-106553000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr4:106525400-106558600	Weak transcription	Fetal Intestine Large	intestine
3	chr4:106527200-106559000	Weak transcription	Fetal Intestine Small	intestine
4	chr4:106540600-106553800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:106545200-106577800	Weak transcription	Pancreas	Pancrea
6	chr4:106545800-106558600	Weak transcription	Left Ventricle	heart
7	chr4:106546000-106553800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:106546000-106555800	Weak transcription	Fetal Lung	lung
9	chr4:106546000-106558200	Weak transcription	Brain Substantia Nigra	brain
10	chr4:106546200-106554000	Weak transcription	Small Intestine	intestine
11	chr4:106547000-106553800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:106549400-106555200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr4:106549600-106555600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr4:106549600-106558600	Weak transcription	Gastric	stomach
15	chr4:106549800-106553400	Weak transcription	Stomach Mucosa	stomach
16	chr4:106550600-106559400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:106551600-106552800	Enhancers	Rectal Smooth Muscle	rectum
18	chr4:106551600-106553200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:106551600-106555200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:106551800-106552800	Enhancers	Colon Smooth Muscle	Colon
21	chr4:106551800-106553200	Enhancers	Fetal Kidney	kidney
22	chr4:106551800-106554000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:106551800-106554800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:106551800-106555400	Enhancers	HMEC	breast
25	chr4:106552200-106552800	Enhancers	Brain Cingulate Gyrus	brain
26	chr4:106552200-106552800	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr4:106552200-106553200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:106552400-106552800	Enhancers	Brain Anterior Caudate	brain
29	chr4:106552400-106555200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr4:106552400-106555600	Weak transcription	Brain Hippocampus Middle	brain
31	chr4:106552400-106555600	Enhancers	GM12878-XiMat	blood
32	chr4:106552400-106558400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr4:106552600-106553000	Enhancers	NHEK	skin
34	chr4:106552600-106554200	Weak transcription	Fetal Heart	heart
35	chr4:106552600-106555000	Weak transcription	Fetal Brain Male	brain

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