Variant report

Variant	rs4147225
Chromosome Location	chr9:8859138-8859139
allele	A/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	CTBP2	chr9:8857170-8859227	H1-hESC	embryonic stem cell:	n/a	n/a
2	JUND	chr9:8858334-8859255	H1-hESC	embryonic stem cell:	n/a	chr9:8858879-8858888
3	POLR2A	chr9:8856850-8859316	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr9:8856879-8859283	H1-neurons	neurons:	n/a	n/a
5	ZNF263	chr9:8856641-8860520	HEK293-T-REx	kidney:	n/a	chr9:8858101-8858122 chr9:8859812-8859821 chr9:8858020-8858029
6	REST	chr9:8854700-8859485	H1-neurons	neurons:	n/a	chr9:8858684-8858697 chr9:8858684-8858697 chr9:8858577-8858585 chr9:8858768-8858781 chr9:8854758-8854765 chr9:8858410-8858423
7	CREB1	chr9:8858603-8859142	H1-hESC	embryonic stem cell:	n/a	chr9:8858877-8858890
8	ATF2	chr9:8858467-8859172	H1-hESC	embryonic stem cell:	n/a	chr9:8858876-8858890 chr9:8858878-8858889

Variant related genes	Relation type
PTPRD	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10759007	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12236086	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1991863	0.83[AMR][1000 genomes];0.89[EUR][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	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv892235	chr9:8700396-8865925	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1025800	chr9:8712487-9030627	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv539980	chr9:8712487-9030627	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv892236	chr9:8745520-8870553	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1015898	chr9:8753534-9011443	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8853600-8859200	Active TSS	Brain Cingulate Gyrus	brain
2	chr9:8853800-8859600	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr9:8854200-8859200	Active TSS	Brain Substantia Nigra	brain
4	chr9:8854600-8859200	Active TSS	Brain Angular Gyrus	brain
5	chr9:8854600-8859400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:8856400-8859200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
7	chr9:8856400-8859200	Active TSS	Fetal Kidney	kidney
8	chr9:8856600-8859200	Active TSS	H9 Cell Line	embryonic stem cell
9	chr9:8856800-8859400	Active TSS	Rectal Smooth Muscle	rectum
10	chr9:8857200-8859200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:8857400-8859200	Active TSS	Brain Hippocampus Middle	brain
12	chr9:8857400-8859200	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr9:8857400-8859600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
14	chr9:8858200-8859200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
15	chr9:8858400-8859200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
16	chr9:8858400-8859200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
17	chr9:8858400-8859200	Flanking Bivalent TSS/Enh	NH-A	brain
18	chr9:8858400-8859600	Flanking Active TSS	Fetal Brain Male	brain
19	chr9:8858600-8859200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr9:8858600-8859200	Enhancers	Placenta Amnion	Placenta Amnion
21	chr9:8858600-8859200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr9:8858800-8859200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
23	chr9:8858800-8859200	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:8858800-8859200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:8858800-8859200	Enhancers	Primary hematopoietic stem cells	blood
26	chr9:8858800-8859200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
27	chr9:8858800-8859200	Flanking Active TSS	Fetal Muscle Trunk	muscle
28	chr9:8858800-8859200	Flanking Active TSS	Fetal Muscle Leg	muscle
29	chr9:8858800-8859200	Flanking Active TSS	Fetal Stomach	stomach
30	chr9:8858800-8859200	Enhancers	Lung	lung
31	chr9:8858800-8859400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:8858800-8859400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr9:8858800-8859400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:8858800-8859400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr9:8858800-8859400	Flanking Active TSS	Brain Germinal Matrix	brain
36	chr9:8858800-8859600	Flanking Bivalent TSS/Enh	Fetal Lung	lung
37	chr9:8858800-8871400	Enhancers	Fetal Heart	heart
38	chr9:8859000-8859200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr9:8859000-8859200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:8859000-8859200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
41	chr9:8859000-8859200	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
42	chr9:8859000-8859200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr9:8859000-8859200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr9:8859000-8859200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr9:8859000-8859200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr9:8859000-8859200	Active TSS	Colonic Mucosa	Colon
47	chr9:8859000-8859200	Flanking Active TSS	Fetal Brain Female	brain
48	chr9:8859000-8859200	Flanking Active TSS	Ovary	ovary
49	chr9:8859000-8859200	Bivalent Enhancer	NHLF	lung
50	chr9:8859000-8859400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links