Variant report

Variant	rs4975268
Chromosome Location	chr4:129751768-129751769
allele	G/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	POLR2A	chr4:129751584-129753214	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
JADE1	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10017436	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11098987	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11724119	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1425618	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1648062	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs167618	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17013778	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016294	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs318504	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs318505	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs318555	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs318556	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4975263	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975264	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4975266	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4975270	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55829553	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62317868	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6833391	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6844446	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][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	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1020801	chr4:129658178-129778086	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv537248	chr4:129658178-129778086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv517249	chr4:129738328-129927804	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4975268	PHF17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129734400-129756400	Weak transcription	Aorta	Aorta
2	chr4:129735400-129752200	Weak transcription	Fetal Brain Female	brain
3	chr4:129741800-129752000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:129746600-129751800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr4:129746600-129752000	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr4:129746600-129752800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr4:129746600-129761800	Strong transcription	Dnd41	blood
8	chr4:129746800-129751800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:129746800-129757000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:129746800-129770200	Weak transcription	HMEC	breast
11	chr4:129747000-129752000	Weak transcription	Fetal Brain Male	brain
12	chr4:129747000-129752200	Weak transcription	Hela-S3	cervix
13	chr4:129747000-129766600	Weak transcription	NHEK	skin
14	chr4:129747200-129751800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:129747200-129751800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr4:129747200-129752000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:129747400-129751800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr4:129747400-129751800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr4:129747400-129752000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr4:129747400-129752000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:129747400-129752000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:129747400-129752000	Weak transcription	NH-A	brain
23	chr4:129747400-129752200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:129747400-129752200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr4:129747400-129752400	Weak transcription	HSMMtube	muscle
26	chr4:129747400-129754200	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr4:129747400-129756600	Weak transcription	Esophagus	oesophagus
28	chr4:129747400-129761600	Weak transcription	Placenta	Placenta
29	chr4:129747600-129751800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr4:129747600-129751800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr4:129747600-129752000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:129747600-129752000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr4:129748000-129761600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr4:129748200-129751800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:129748200-129752000	Weak transcription	Brain Angular Gyrus	brain
36	chr4:129748400-129751800	Weak transcription	Liver	Liver
37	chr4:129748400-129752000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:129748600-129751800	Weak transcription	Brain Hippocampus Middle	brain
39	chr4:129748600-129751800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr4:129748600-129751800	Weak transcription	HSMM	muscle
41	chr4:129748600-129752000	Weak transcription	Primary B cells from cord blood	blood
42	chr4:129748600-129752000	Weak transcription	Brain Substantia Nigra	brain
43	chr4:129748800-129751800	Weak transcription	Fetal Intestine Large	intestine
44	chr4:129748800-129751800	Weak transcription	Fetal Stomach	stomach
45	chr4:129748800-129752000	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr4:129749000-129754200	Genic enhancers	H1 Cell Line	embryonic stem cell
47	chr4:129749200-129751800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr4:129749200-129751800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr4:129749200-129752000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr4:129749200-129752000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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