Variant report

Variant	rs13136122
Chromosome Location	chr4:704602-704603
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:703233..707351-chr4:710441..713114,3	MCF-7	breast:
2	chr4:704517..706514-chr4:717947..720061,2	K562	blood:
3	chr4:672222..675225-chr4:704052..707377,3	K562	blood:
4	chr4:697170..699923-chr4:703607..707552,5	K562	blood:
5	chr4:671675..674589-chr4:702337..705311,3	MCF-7	breast:
6	chr4:687290..688821-chr4:702192..704645,2	MCF-7	breast:
7	chr4:702491..704848-chr4:710046..712151,2	K562	blood:

Variant related genes	Relation type
ENSG00000185619	Chromatin interaction
ENSG00000215375	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs4076064	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
6	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS 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	104 gene(s)	inside rSNPs	diseases
10	nsv593206	chr4:625962-735150	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	esv1829397	chr4:655939-1041957	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
12	nsv829834	chr4:665477-775524	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv593209	chr4:686563-747810	Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv870115	chr4:692811-733794	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs13136122	RP11-440L14.1	cis	Esophagus Mucosa	GTEx
rs13136122	AC139887.4	cis	Skin Sun Exposed Lower leg	GTEx
rs13136122	AC139887.4	cis	Nerve Tibial	GTEx
rs13136122	RP11-440L14.1	cis	Skin Sun Exposed Lower leg	GTEx
rs13136122	PCGF3	cis	Artery Tibial	GTEx
rs13136122	RP11-440L14.1	cis	Artery Tibial	GTEx
rs13136122	PCGF3	Cis_1M	lymphoblastoid	RTeQTL
rs13136122	PCGF3	cis	Nerve Tibial	GTEx
rs13136122	PCGF3	cis	Muscle Skeletal	GTEx
rs13136122	PCGF3	cis	Adipose Subcutaneous	GTEx
rs13136122	AC139887.4	cis	lung	GTEx
rs13136122	RP11-440L14.1	cis	Nerve Tibial	GTEx
rs13136122	PCGF3	cis	Esophagus Mucosa	GTEx
rs13136122	RP11-440L14.1	cis	Adipose Subcutaneous	GTEx
rs13136122	AC139887.4	cis	Thyroid	GTEx
rs13136122	RP11-440L14.1	cis	Esophagus Muscularis	GTEx
rs13136122	AC139887.4	cis	Adipose Subcutaneous	GTEx
rs13136122	PCGF3	cis	Heart Left Ventricle	GTEx
rs13136122	PCGF3	cis	Esophagus Muscularis	GTEx
rs13136122	PCGF3	cis	Skin Sun Exposed Lower leg	GTEx
rs13136122	PCGF3	cis	lung	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:701000-705800	Weak transcription	Fetal Kidney	kidney
2	chr4:701200-713400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:701200-713400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr4:701200-714600	Weak transcription	NHDF-Ad	bronchial
5	chr4:701200-724400	Weak transcription	Aorta	Aorta
6	chr4:701400-705000	Enhancers	Pancreas	Pancrea
7	chr4:701400-705200	Strong transcription	Fetal Intestine Small	intestine
8	chr4:701400-714000	Weak transcription	HMEC	breast
9	chr4:701400-715200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr4:701400-724400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr4:701400-724800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr4:701600-716800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:701800-705000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:702000-705000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:702000-705000	Genic enhancers	Fetal Muscle Trunk	muscle
16	chr4:702200-705000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:702200-705000	Genic enhancers	Spleen	Spleen
18	chr4:702200-754800	Weak transcription	Hela-S3	cervix
19	chr4:702400-704800	Enhancers	Brain Hippocampus Middle	brain
20	chr4:702400-705000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:702400-708000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr4:702400-714600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr4:702400-720000	Weak transcription	Brain Substantia Nigra	brain
24	chr4:702400-720200	Weak transcription	NH-A	brain
25	chr4:702600-704800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:702600-705000	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr4:702600-706000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:702600-707800	Weak transcription	NHLF	lung
29	chr4:702600-708000	Weak transcription	Colonic Mucosa	Colon
30	chr4:702600-708600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:702600-715800	Weak transcription	Liver	Liver
32	chr4:702600-716800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:702600-724400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr4:702800-705000	Genic enhancers	Dnd41	blood
35	chr4:702800-705200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:702800-707200	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr4:702800-707800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr4:702800-708000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:702800-714600	Weak transcription	Stomach Mucosa	stomach
40	chr4:702800-715000	Weak transcription	GM12878-XiMat	blood
41	chr4:702800-726600	Weak transcription	Primary B cells from cord blood	blood
42	chr4:703000-708800	Strong transcription	Fetal Stomach	stomach
43	chr4:703000-711400	Weak transcription	Fetal Heart	heart
44	chr4:703000-714000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:703000-714000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr4:703000-716600	Weak transcription	Fetal Lung	lung
47	chr4:703400-704800	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr4:703400-704800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr4:703400-705000	Strong transcription	Primary B cells from peripheral blood	blood
50	chr4:703400-705000	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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