Variant report

Variant	rs6837180
Chromosome Location	chr4:698292-698293
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CCNT2	chr4:698263-698583	K562	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:693289..694985-chr4:696803..698794,2	MCF-7	breast:
2	chr4:691381..694386-chr4:695506..698892,4	K562	blood:
3	chr4:694824..697589-chr4:697861..699485,2	K562	blood:
4	chr4:697549..703820-chr4:770860..775722,9	K562	blood:
5	chr4:673479..675144-chr4:696764..699498,2	K562	blood:
6	chr4:672883..676399-chr4:697081..701106,5	MCF-7	breast:
7	chr4:672428..678608-chr4:693605..699154,7	MCF-7	breast:
8	chr4:666292..671732-chr4:694079..701503,8	MCF-7	breast:
9	chr4:681693..683683-chr4:698278..699853,2	K562	blood:
10	chr4:666295..671517-chr4:698228..703248,8	MCF-7	breast:
11	chr4:680242..683670-chr4:697022..701034,8	MCF-7	breast:
12	chr4:696628..698929-chr4:713327..715075,2	MCF-7	breast:
13	chr4:681383..683193-chr4:698223..700658,3	K562	blood:

No data

Variant related genes	Relation type
PCGF3	TF binding region
ENSG00000169020	Chromatin interaction
ENSG00000215375	Chromatin interaction
ENSG00000169026	Chromatin interaction
ENSG00000249592	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12510790	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs9332466	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 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
15	nsv10414	chr4:696527-701955	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6837180	PCGF3	cis	Whole Blood	GTEx
rs6837180	RP11-440L14.1	cis	Whole Blood	GTEx
rs6837180	RP11-440L14.1	cis	Nerve Tibial	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:683600-699000	Weak transcription	Right Atrium	heart
2	chr4:684200-699000	Weak transcription	Right Ventricle	heart
3	chr4:693400-698800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:693600-698800	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr4:693600-698800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr4:693600-698800	Weak transcription	Hela-S3	cervix
7	chr4:693800-698600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:693800-698800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr4:693800-698800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr4:693800-698800	Weak transcription	Liver	Liver
11	chr4:694000-698800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:694000-698800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:694000-698800	Weak transcription	Primary B cells from cord blood	blood
14	chr4:694000-698800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr4:694000-698800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:694000-698800	Weak transcription	Fetal Thymus	thymus
17	chr4:694000-698800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr4:694000-699000	Weak transcription	GM12878-XiMat	blood
19	chr4:694200-698400	Weak transcription	Colonic Mucosa	Colon
20	chr4:694200-698800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:694200-699000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr4:694400-698600	Weak transcription	Primary B cells from peripheral blood	blood
23	chr4:694400-698600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr4:694600-698600	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr4:694600-698800	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr4:694800-698800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr4:694800-699000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr4:695000-698600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr4:695000-699000	Weak transcription	Brain Angular Gyrus	brain
30	chr4:696000-699000	Enhancers	Stomach Mucosa	stomach
31	chr4:697000-698800	Weak transcription	NHEK	skin
32	chr4:697000-699000	Weak transcription	Fetal Intestine Large	intestine
33	chr4:697000-699000	Enhancers	K562	blood
34	chr4:697200-699000	Enhancers	Spleen	Spleen
35	chr4:697400-698800	Weak transcription	Brain Anterior Caudate	brain
36	chr4:697400-699000	Weak transcription	Brain Hippocampus Middle	brain
37	chr4:697600-698400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr4:697600-699000	Enhancers	Placenta	Placenta
39	chr4:697800-698400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr4:697800-699000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr4:697800-699000	Enhancers	Gastric	stomach
42	chr4:698000-698400	Flanking Bivalent TSS/Enh	HepG2	liver
43	chr4:698000-699000	Enhancers	Esophagus	oesophagus
44	chr4:698200-698400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr4:698200-698800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr4:698200-699000	Enhancers	Primary T cells fromperipheralblood	blood
47	chr4:698200-699000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:698200-699000	Enhancers	Brain Inferior Temporal Lobe	brain

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