Variant report

Variant	rs12719770
Chromosome Location	chr4:507001-507002
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:506858..508809-chr4:513125..514972,2	MCF-7	breast:
2	chr4:492460..494602-chr4:506336..508416,3	MCF-7	breast:
3	chr4:493744..499975-chr4:504792..509084,10	K562	blood:
4	chr4:491400..498728-chr4:498838..507098,13	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF721-3	chr4:506428-508061	NONHSAT094558

Variant related genes	Relation type
ENSG00000182903	Chromatin interaction
ENSG00000174227	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10029096	0.92[CEU][hapmap];0.83[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10029104	0.82[EUR][1000 genomes]
rs13114024	0.92[CEU][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13114026	0.86[TSI][hapmap]
rs13115344	0.85[CEU][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13124714	0.83[EUR][1000 genomes]
rs13131404	0.92[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13136656	0.81[EUR][1000 genomes]
rs13150531	0.91[TSI][hapmap]
rs28609510	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34872561	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35270677	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35334779	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35956476	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4324510	0.85[CEU][hapmap]
rs4365672	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4380466	0.92[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4488886	0.91[CEU][hapmap]
rs4499656	0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4504200	0.92[CEU][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4616693	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57834329	0.81[EUR][1000 genomes]
rs6818642	0.92[CEU][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7666226	0.91[TSI][hapmap]
rs7666425	0.91[TSI][hapmap]
rs7672868	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs7678962	0.91[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1001899	chr4:68809-517736	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv532703	chr4:72447-614414	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	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
7	nsv532704	chr4:85040-628550	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv1010829	chr4:147570-547070	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv536970	chr4:147570-547070	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12719770	PIGG	cis	brain	BrainEAC
rs12719770	ZNF721	cis	parietal	SCAN
rs12719770	PIGG	cis	Liver	GTEx
rs12719770	HSS00262248	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:493600-520000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:494400-521400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr4:494400-531000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:494400-533200	Strong transcription	Placenta	Placenta
5	chr4:494400-534600	Weak transcription	Fetal Heart	heart
6	chr4:494600-507200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:494600-525600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:494600-532000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr4:494600-533000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:494600-533200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:494600-533200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:494800-513200	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr4:494800-513400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:494800-513600	Strong transcription	Primary B cells from peripheral blood	blood
15	chr4:495000-511600	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr4:495000-533000	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:495200-507800	Strong transcription	Fetal Intestine Small	intestine
18	chr4:495200-533000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr4:495200-534000	Strong transcription	Fetal Stomach	stomach
20	chr4:495400-513600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:496200-507200	Weak transcription	Psoas Muscle	Psoas
22	chr4:496400-533000	Strong transcription	Fetal Brain Female	brain
23	chr4:496800-532000	Strong transcription	Dnd41	blood
24	chr4:498400-513800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:498800-513000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:499400-513600	Strong transcription	Brain Germinal Matrix	brain
27	chr4:499600-526600	Strong transcription	Primary B cells from cord blood	blood
28	chr4:502200-507200	Weak transcription	HSMM	muscle
29	chr4:502200-507400	Weak transcription	NHDF-Ad	bronchial
30	chr4:502200-507600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:502200-507800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr4:502400-507400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr4:502600-509000	Weak transcription	Fetal Kidney	kidney
34	chr4:502800-508200	Weak transcription	Hela-S3	cervix
35	chr4:502800-512600	Strong transcription	Fetal Thymus	thymus
36	chr4:503000-507400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr4:503000-511200	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr4:503000-530600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr4:503000-531600	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr4:503200-530800	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr4:503400-507200	Weak transcription	Colonic Mucosa	Colon
42	chr4:503600-507200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr4:503600-509000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr4:503600-532000	Strong transcription	Primary T cells from cord blood	blood
45	chr4:503800-507400	Weak transcription	A549	lung
46	chr4:503800-507400	Weak transcription	HUVEC	blood vessel
47	chr4:503800-532800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr4:504000-507200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr4:504000-508800	Weak transcription	Small Intestine	intestine
50	chr4:504000-509200	Weak transcription	Colon Smooth Muscle	Colon

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