Variant report

Variant	rs67786546
Chromosome Location	chr21:46285416-46285417
allele	C/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	chr21:46285303-46286949	HepG2	liver:	n/a	n/a
2	SPI1	chr21:46285338-46286022	GM12878	blood:	n/a	n/a
3	POLR2A	chr21:46285200-46285519	HepG2	liver:	n/a	n/a
4	POLR2A	chr21:46285382-46286028	HL-60	blood:	n/a	n/a
5	POLR2A	chr21:46285352-46285646	HUVEC	blood vessel:	n/a	n/a
6	SPI1	chr21:46285354-46286055	HL-60	blood:	n/a	n/a
7	MAX	chr21:46285011-46285886	MCF-7	breast:	n/a	chr21:46285293-46285304 chr21:46285294-46285304 chr21:46285294-46285303 chr21:46285295-46285302 chr21:46285840-46285849
8	POLR2A	chr21:46285329-46285841	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:46280368..46282945-chr21:46283456..46285604,4	MCF-7	breast:
2	chr21:46234824..46239565-chr21:46284858..46289652,5	K562	blood:
3	chr21:46282547..46285422-chr21:46309419..46311568,2	K562	blood:
4	chr21:45930623..45933218-chr21:46282665..46285532,2	MCF-7	breast:
5	chr21:46274905..46276457-chr21:46283894..46285475,2	K562	blood:
6	chr21:46220733..46222651-chr21:46282710..46285466,2	K562	blood:
7	chr21:46283208..46285602-chr21:46427466..46429012,2	MCF-7	breast:
8	chr21:46236678..46239215-chr21:46284689..46286960,3	MCF-7	breast:

Variant related genes	Relation type
PTTG1IP	TF binding region
ENSG00000236519	Chromatin interaction
ENSG00000184787	Chromatin interaction
ENSG00000183255	Chromatin interaction
ENSG00000184900	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs13050333	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13050968	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13053009	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2117340	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2117341	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2277811	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34940823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35207173	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35871743	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3810586	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66467973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7279563	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73238097	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers 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	51 gene(s)	inside rSNPs	diseases
3	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv913964	chr21:46223847-46298869	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv913962	chr21:46223847-46321172	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv913965	chr21:46223847-46321172	Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv1058550	chr21:46227163-46317934	Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv913968	chr21:46249752-46301008	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1060233	chr21:46254075-46323401	Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv1056513	chr21:46254075-46442759	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv913969	chr21:46279505-46472929	Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv544479	chr21:46280467-46323401	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
13	nsv470907	chr21:46283669-46306161	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
14	nsv459299	chr21:46283669-46311264	Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
15	nsv459300	chr21:46283669-46311264	Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
16	nsv587814	chr21:46283669-46311264	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs67786546	PTTG1IP	cis	lung	GTEx
rs67786546	PTTG1IP	cis	Thyroid	GTEx
rs67786546	PTTG1IP	cis	Artery Tibial	GTEx
rs67786546	PTTG1IP	cis	Artery Aorta	GTEx
rs67786546	PTTG1IP	cis	Heart Left Ventricle	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46267400-46286600	Strong transcription	Fetal Stomach	stomach
2	chr21:46267600-46287000	Strong transcription	Brain Germinal Matrix	brain
3	chr21:46268200-46285800	Strong transcription	Fetal Muscle Leg	muscle
4	chr21:46268600-46285800	Strong transcription	Liver	Liver
5	chr21:46268600-46286000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr21:46268600-46286600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr21:46268800-46286600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr21:46268800-46286600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr21:46268800-46286600	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr21:46269400-46285800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr21:46271400-46286800	Weak transcription	Psoas Muscle	Psoas
12	chr21:46273000-46286600	Strong transcription	H9 Cell Line	embryonic stem cell
13	chr21:46273400-46285600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr21:46275600-46290600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr21:46276400-46286000	Strong transcription	K562	blood
16	chr21:46277800-46286600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr21:46278200-46285600	Strong transcription	Aorta	Aorta
18	chr21:46278200-46286400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
19	chr21:46278400-46289600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr21:46279400-46286600	Weak transcription	Fetal Brain Male	brain
21	chr21:46279400-46288400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr21:46279600-46288800	Weak transcription	Fetal Kidney	kidney
23	chr21:46279800-46287600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr21:46280600-46285600	Genic enhancers	Primary T cells fromperipheralblood	blood
25	chr21:46281000-46285600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr21:46281400-46286000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr21:46282000-46285800	Strong transcription	A549	lung
28	chr21:46282000-46286000	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr21:46282200-46285800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr21:46282200-46286000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr21:46282200-46286200	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr21:46283000-46285600	Strong transcription	Colonic Mucosa	Colon
33	chr21:46283000-46286000	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr21:46283400-46285600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr21:46283400-46285600	Strong transcription	Hela-S3	cervix
36	chr21:46283400-46285800	Strong transcription	Fetal Muscle Trunk	muscle
37	chr21:46283400-46285800	Strong transcription	Placenta Amnion	Placenta Amnion
38	chr21:46283400-46286200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
39	chr21:46283400-46288800	Strong transcription	NHEK	skin
40	chr21:46283600-46285600	Strong transcription	Brain Angular Gyrus	brain
41	chr21:46283600-46285800	Strong transcription	Fetal Brain Female	brain
42	chr21:46283600-46286000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr21:46283800-46285600	Weak transcription	Fetal Heart	heart
44	chr21:46284000-46288400	Genic enhancers	Spleen	Spleen
45	chr21:46284000-46289000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr21:46284600-46285600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr21:46284600-46285600	Genic enhancers	Lung	lung
48	chr21:46284600-46287600	Genic enhancers	Fetal Intestine Large	intestine
49	chr21:46284600-46287800	Genic enhancers	Gastric	stomach
50	chr21:46284800-46285600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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