Variant report

Variant	rs4823000
Chromosome Location	chr22:29379891-29379892
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	FOXA1	chr22:29379662-29380112	T-47D	breast:	n/a	n/a
2	TEAD4	chr22:29379778-29380153	H1-hESC	embryonic stem cell:	n/a	n/a
3	CEBPB	chr22:29379722-29380415	MCF-7	breast:	n/a	chr22:29379906-29379919 chr22:29380212-29380223
4	FOXA1	chr22:29379784-29380056	T-47D	breast:	n/a	n/a
5	MAX	chr22:29379890-29380064	H1-hESC	embryonic stem cell:	n/a	n/a
6	CEBPB	chr22:29379839-29380340	H1-hESC	embryonic stem cell:	n/a	chr22:29379906-29379919 chr22:29380212-29380223
7	CEBPB	chr22:29379640-29380437	MCF-7	breast:	n/a	chr22:29379906-29379919 chr22:29380212-29380223

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29379528..29381161-chr22:29385924..29388369,2	MCF-7	breast:
2	chr22:29374740..29376458-chr22:29379657..29381475,2	K562	blood:

Variant related genes	Relation type
ZNRF3	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11912198	0.89[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs12169126	0.91[ASN][1000 genomes]
rs12627758	0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12628457	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12628579	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16986951	0.82[EUR][1000 genomes]
rs41341948	0.85[GIH][hapmap];0.82[MEX][hapmap]
rs4823001	0.82[MEX][hapmap]
rs5752839	0.92[JPT][hapmap]
rs5752842	0.92[JPT][hapmap]
rs5752850	0.89[ASW][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs5752851	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs5762891	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs5762893	1.00[JPT][hapmap]
rs5762900	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs5762906	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs5762907	0.92[JPT][hapmap]
rs5762919	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs5762926	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs5762931	0.80[LWK][hapmap]
rs5762938	0.89[ASW][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs61697201	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs725281	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7288513	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs7290364	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs8140640	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9306461	1.00[JPT][hapmap]
rs9625645	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs974370	0.93[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.99[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	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29365800-29394800	Weak transcription	Pancreas	Pancrea
2	chr22:29373400-29381400	Weak transcription	Fetal Stomach	stomach
3	chr22:29373400-29390800	Weak transcription	Hela-S3	cervix
4	chr22:29373600-29400200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr22:29374200-29381600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr22:29374200-29383000	Weak transcription	Ovary	ovary
7	chr22:29374400-29395200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr22:29374600-29380600	Weak transcription	Right Atrium	heart
9	chr22:29374600-29381400	Enhancers	Liver	Liver
10	chr22:29374600-29385000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr22:29374600-29395600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr22:29374600-29400000	Weak transcription	Right Ventricle	heart
13	chr22:29374600-29401200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr22:29374800-29384400	Weak transcription	Osteobl	bone
15	chr22:29375200-29385200	Weak transcription	Brain Substantia Nigra	brain
16	chr22:29375600-29383000	Weak transcription	Left Ventricle	heart
17	chr22:29375600-29390800	Weak transcription	NHDF-Ad	bronchial
18	chr22:29375800-29381400	Weak transcription	Fetal Intestine Small	intestine
19	chr22:29375800-29383000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr22:29375800-29383200	Weak transcription	Brain Hippocampus Middle	brain
21	chr22:29375800-29383200	Weak transcription	Fetal Intestine Large	intestine
22	chr22:29375800-29395400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr22:29376600-29383600	Weak transcription	K562	blood
24	chr22:29376600-29384200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr22:29377600-29380800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr22:29377800-29380800	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr22:29378000-29380600	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr22:29378000-29381200	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr22:29378000-29383600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr22:29378000-29385400	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr22:29378200-29380400	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr22:29378200-29380800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr22:29378600-29380000	Enhancers	Fetal Heart	heart
34	chr22:29378600-29380400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr22:29378600-29381000	Enhancers	HepG2	liver
36	chr22:29378600-29381400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr22:29378600-29381800	Enhancers	HSMMtube	muscle
38	chr22:29378800-29380800	Enhancers	HSMM	muscle
39	chr22:29378800-29381200	Enhancers	HMEC	breast
40	chr22:29378800-29381200	Enhancers	NHEK	skin
41	chr22:29378800-29381600	Enhancers	Fetal Muscle Leg	muscle
42	chr22:29378800-29384200	Weak transcription	A549	lung
43	chr22:29379000-29380600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr22:29379000-29381000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr22:29379000-29381200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr22:29379000-29381200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr22:29379000-29381200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr22:29379000-29381800	Enhancers	Placenta	Placenta
49	chr22:29379000-29383200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr22:29379000-29383400	Enhancers	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links