Variant report

Variant	rs28450817
Chromosome Location	chr22:29600333-29600334
allele	C/G
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	WRNIP1	chr22:29599643-29600581	GM12878	blood:	n/a	n/a
2	CTCF	chr22:29600200-29600350	GM06990	blood:	n/a	n/a
3	EBF1	chr22:29599825-29600930	GM12878	blood:	n/a	chr22:29600601-29600610 chr22:29600599-29600612 chr22:29600600-29600611 chr22:29600600-29600610 chr22:29600601-29600610
4	BHLHE40	chr22:29600224-29600481	GM12878	blood:	n/a	n/a
5	CTCF	chr22:29600241-29600801	GM12878	blood:	n/a	n/a
6	TBP	chr22:29599630-29601290	GM12878	blood:	n/a	n/a
7	RUNX3	chr22:29600229-29601429	GM12878	blood:	n/a	n/a
8	CTCF	chr22:29600321-29600473	GM19239	blood:	n/a	n/a
9	CTCF	chr22:29600309-29600432	GM19238	blood:	n/a	n/a
10	RFX5	chr22:29600299-29600614	GM12878	blood:	n/a	n/a
11	CTCF	chr22:29600260-29600410	GM12875	blood:	n/a	n/a
12	POLR2A	chr22:29599562-29605938	PBDE	blood:	n/a	n/a
13	GATA1	chr22:29599489-29600342	PBDE	blood:	n/a	n/a
14	CTCF	chr22:29600200-29600350	HEK293	kidney:	n/a	n/a
15	EBF1	chr22:29599729-29601175	GM12878	blood:	n/a	chr22:29600601-29600610 chr22:29600599-29600612 chr22:29600600-29600611 chr22:29600600-29600610 chr22:29600601-29600610
16	CTCF	chr22:29600200-29600350	GM12870	blood:	n/a	n/a
17	CTCF	chr22:29600240-29600390	Caco-2	colon:	n/a	n/a
18	STAT5A	chr22:29599776-29600342	GM12878	blood:	n/a	n/a
19	CTCF	chr22:29600320-29600470	GM12874	blood:	n/a	n/a
20	CTCF	chr22:29600260-29600410	GM12872	blood:	n/a	n/a
21	POLR2A	chr22:29597149-29601230	GM12878	blood:	n/a	n/a
22	EBF1	chr22:29599765-29600909	GM12878	blood:	n/a	chr22:29600601-29600610 chr22:29600599-29600612 chr22:29600600-29600611 chr22:29600600-29600610 chr22:29600601-29600610
23	CTCF	chr22:29600200-29600350	GM12868	blood:	n/a	n/a
24	CTCF	chr22:29600260-29600410	GM12871	blood:	n/a	n/a
25	POLR2A	chr22:29597600-29600699	GM12878	blood:	n/a	n/a
26	CTCF	chr22:29600320-29600470	GM12872	blood:	n/a	n/a
27	CTCF	chr22:29600260-29600410	GM12874	blood:	n/a	n/a
28	CTCF	chr22:29600320-29600470	GM06990	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:29598167..29600634-chr22:29663372..29666044,2	K562	blood:
2	chr22:29289372..29291896-chr22:29597783..29600686,2	MCF-7	breast:
3	chr22:29599772..29601516-chr22:29662820..29665325,2	K562	blood:

Variant related genes	Relation type
EMID1	TF binding region
ENSG00000100263	Chromatin interaction
ENSG00000182944	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs16987011	1.00[AMR][1000 genomes]
rs16987087	1.00[AMR][1000 genomes]
rs28711804	1.00[AMR][1000 genomes]
rs416358	1.00[AMR][1000 genomes]
rs58690800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6005989	1.00[AMR][1000 genomes]
rs6006059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61500482	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73397056	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73397059	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73397080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73399009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73399038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8138179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9625701	1.00[AMR][1000 genomes]
rs9625702	1.00[AMR][1000 genomes]
rs9625723	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv524483	chr22:29525126-29630337	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv914958	chr22:29586058-29620599	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv1809952	chr22:29595349-29661434	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29594800-29600800	Weak transcription	Pancreas	Pancrea
2	chr22:29596400-29601600	Enhancers	Spleen	Spleen
3	chr22:29597000-29601000	Enhancers	Primary hematopoietic stem cells	blood
4	chr22:29597000-29601400	Enhancers	Fetal Thymus	thymus
5	chr22:29597800-29601000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr22:29597800-29601400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr22:29597800-29601800	Flanking Active TSS	Dnd41	blood
8	chr22:29598200-29600400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr22:29598200-29600600	Enhancers	Thymus	Thymus
10	chr22:29598200-29600800	Enhancers	H1 Cell Line	embryonic stem cell
11	chr22:29598400-29601600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr22:29598800-29600800	Enhancers	Duodenum Mucosa	Duodenum
13	chr22:29598800-29601000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr22:29598800-29601400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr22:29598800-29602000	Weak transcription	Brain Angular Gyrus	brain
16	chr22:29599000-29600400	Weak transcription	Fetal Kidney	kidney
17	chr22:29599000-29600600	Weak transcription	Right Ventricle	heart
18	chr22:29599000-29600800	Weak transcription	Colonic Mucosa	Colon
19	chr22:29599000-29601000	Weak transcription	Adipose Nuclei	Adipose
20	chr22:29599000-29601200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr22:29599000-29601200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr22:29599000-29601400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr22:29599000-29601400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr22:29599000-29601400	Weak transcription	Liver	Liver
25	chr22:29599000-29601400	Weak transcription	Brain Hippocampus Middle	brain
26	chr22:29599000-29601400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr22:29599000-29601400	Weak transcription	Lung	lung
28	chr22:29599000-29601400	Weak transcription	NH-A	brain
29	chr22:29599000-29601600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr22:29599000-29601600	Weak transcription	Esophagus	oesophagus
31	chr22:29599000-29601600	Weak transcription	Left Ventricle	heart
32	chr22:29599000-29601600	Weak transcription	Right Atrium	heart
33	chr22:29599200-29600600	Weak transcription	Fetal Stomach	stomach
34	chr22:29599200-29601000	Weak transcription	Fetal Intestine Large	intestine
35	chr22:29599200-29601000	Weak transcription	Placenta	Placenta
36	chr22:29599200-29601200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr22:29599200-29601400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr22:29599200-29602200	Weak transcription	Small Intestine	intestine
39	chr22:29599400-29600400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr22:29599400-29600400	Enhancers	K562	blood
41	chr22:29599400-29600600	Weak transcription	Fetal Muscle Trunk	muscle
42	chr22:29599400-29601000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr22:29599400-29601000	Weak transcription	Fetal Lung	lung
44	chr22:29599400-29601200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr22:29599400-29601400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr22:29599400-29601400	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr22:29599400-29601600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr22:29599600-29601000	Weak transcription	Fetal Intestine Small	intestine
49	chr22:29599800-29600400	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr22:29599800-29600800	Enhancers	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links