Variant report

Variant	rs28562547
Chromosome Location	chr4:21950626-21950627
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	CTCF	chr4:21949895-21951210	SK-N-SH	brain:	n/a	chr4:21950602-21950620 chr4:21950604-21950617
2	RAD21	chr4:21950020-21950630	H1-hESC	embryonic stem cell:	n/a	chr4:21950604-21950614 chr4:21950603-21950616 chr4:21950602-21950614
3	MAX	chr4:21949969-21950792	H1-hESC	embryonic stem cell:	n/a	chr4:21950600-21950610
4	CTCF	chr4:21950600-21950750	HMEC	breast:	n/a	chr4:21950602-21950620 chr4:21950604-21950617
5	REST	chr4:21949733-21950644	H1-neurons	neurons:	n/a	chr4:21950004-21950017 chr4:21950306-21950326
6	CTCF	chr4:21950560-21950710	AG09319	gingival:	n/a	chr4:21950602-21950620 chr4:21950604-21950617

Variant related genes	Relation type
ENSG00000250039	TF binding region
KCNIP4	TF binding region

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2007195	0.83[ASN][1000 genomes]
rs2874978	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817467	chr4:21602921-22422816	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2757924	chr4:21873204-21980559	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv2759231	chr4:21873204-21980559	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv428440	chr4:21873204-21980559	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv3524226	chr4:21949654-21951752	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a
6	esv3524227	chr4:21949654-21951752	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:21947600-21950800	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr4:21948000-21951400	Active TSS	Brain Anterior Caudate	brain
3	chr4:21948800-21950800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
4	chr4:21948800-21951000	Active TSS	Ovary	ovary
5	chr4:21949200-21951200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr4:21949400-21951000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
7	chr4:21949400-21951000	Bivalent/Poised TSS	Brain Substantia Nigra	brain
8	chr4:21949400-21951200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr4:21949400-21951200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr4:21949600-21951000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr4:21949600-21951000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
12	chr4:21949600-21951000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
13	chr4:21949600-21951000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:21949600-21951200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
15	chr4:21949600-21951200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:21949600-21951200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
17	chr4:21949600-21951400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr4:21949800-21950800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:21949800-21951000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:21949800-21951000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:21949800-21951000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr4:21949800-21951000	Bivalent Enhancer	Liver	Liver
23	chr4:21949800-21951000	Bivalent/Poised TSS	NHLF	lung
24	chr4:21949800-21951200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:21949800-21951200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:21949800-21951200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
27	chr4:21949800-21951200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
28	chr4:21949800-21951200	Bivalent/Poised TSS	Osteobl	bone
29	chr4:21950000-21950800	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:21950000-21950800	Active TSS	Colon Smooth Muscle	Colon
31	chr4:21950000-21951000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
32	chr4:21950000-21951000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:21950000-21951000	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr4:21950000-21951000	Enhancers	Spleen	Spleen
35	chr4:21950000-21951000	Bivalent/Poised TSS	HepG2	liver
36	chr4:21950000-21951200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
37	chr4:21950000-21951200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:21950000-21951200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:21950000-21951200	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
40	chr4:21950000-21951200	Active TSS	Fetal Kidney	kidney
41	chr4:21950000-21951200	Active TSS	NH-A	brain
42	chr4:21950000-21951400	Active TSS	Brain Angular Gyrus	brain
43	chr4:21950000-21951400	Active TSS	Rectal Smooth Muscle	rectum
44	chr4:21950000-21951600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr4:21950000-21951600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr4:21950200-21950800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr4:21950200-21950800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:21950200-21950800	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
49	chr4:21950200-21950800	Bivalent/Poised TSS	Psoas Muscle	Psoas
50	chr4:21950200-21951000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links