Variant report

Variant	rs2069391
Chromosome Location	chr12:56359878-56359879
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	SIN3AK20	chr12:56359786-56360979	H1-hESC	embryonic stem cell:	n/a	n/a
2	TBP	chr12:56359645-56360107	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr12:56359858-56361309	Hela-S3	cervix:	n/a	n/a
4	SMARCC1	chr12:56359755-56361790	Hela-S3	cervix:	n/a	n/a
5	HEY1	chr12:56359866-56361298	K562	blood:	n/a	n/a
6	POLR2A	chr12:56359849-56361144	K562	blood:	n/a	n/a
7	TAF1	chr12:56359650-56361028	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr12:56359846-56361008	HepG2	liver:	n/a	n/a
9	POLR2A	chr12:56359594-56361350	ECC-1	luminal epithelium:	n/a	n/a
10	JUND	chr12:56359710-56360019	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr12:56359724-56361272	SK-N-MC	brain:	n/a	n/a
12	GTF2F1	chr12:56359762-56359983	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr12:56359840-56359913	Hela-S3	cervix:	n/a	n/a
14	SP1	chr12:56359618-56361191	H1-hESC	embryonic stem cell:	n/a	chr12:56360535-56360547 chr12:56360564-56360576 chr12:56360566-56360575 chr12:56360565-56360575 chr12:56360537-56360546 chr12:56360536-56360545 chr12:56360564-56360576 chr12:56360565-56360575 chr12:56360566-56360575 chr12:56360517-56360538 chr12:56360535-56360547 chr12:56360532-56360546 chr12:56360565-56360574
15	POLR2A	chr12:56359674-56359927	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr12:56359683-56360068	H1-hESC	embryonic stem cell:	n/a	n/a
17	TBP	chr12:56359873-56360831	GM12878	blood:	n/a	n/a
18	BCLAF1	chr12:56359781-56360514	K562	blood:	n/a	n/a
19	SIN3A	chr12:56359099-56361358	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr12:56359580-56359902	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr12:56359332-56361169	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr12:56359847-56360930	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr12:56359595-56360823	H1-hESC	embryonic stem cell:	n/a	n/a
24	ZBTB7A	chr12:56359563-56361328	ECC-1	luminal epithelium:	n/a	n/a
25	POU2F2	chr12:56359779-56360626	GM12891	blood:	n/a	chr12:56359866-56359876 chr12:56359867-56359876 chr12:56359865-56359879 chr12:56359865-56359877 chr12:56359866-56359876 chr12:56359868-56359875 chr12:56359867-56359877 chr12:56360563-56360575 chr12:56359864-56359879 chr12:56359868-56359876
26	POLR2A	chr12:56359835-56360934	K562	blood:	n/a	n/a
27	WRNIP1	chr12:56359857-56360306	GM12878	blood:	n/a	n/a
28	POLR2A	chr12:56359843-56361090	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56351426..56355339-chr12:56358310..56361732,4	K562	blood:
2	chr12:56348195..56352007-chr12:56357444..56361194,9	MCF-7	breast:
3	chr12:56222205..56224922-chr12:56358822..56360561,2	MCF-7	breast:
4	chr12:56132724..56138260-chr12:56359199..56362083,4	MCF-7	breast:
5	chr12:56319178..56327497-chr12:56356755..56363470,19	MCF-7	breast:
6	chr12:56319082..56322613-chr12:56358459..56362927,5	MCF-7	breast:
7	chr12:56359297..56361313-chr17:56079815..56082507,2	MCF-7	breast:
8	chr12:56135390..56138217-chr12:56359317..56362756,4	K562	blood:
9	chr12:56325013..56327160-chr12:56358376..56361876,4	MCF-7	breast:
10	chr12:56208204..56214844-chr12:56359426..56363484,9	MCF-7	breast:
11	chr12:56334256..56336718-chr12:56359485..56361088,3	K562	blood:
12	chr12:56332251..56334580-chr12:56358536..56360583,2	MCF-7	breast:
13	chr12:56319307..56323047-chr12:56359033..56361996,7	K562	blood:
14	chr12:56357871..56361008-chr12:56510432..56513466,3	K562	blood:
15	chr12:56328814..56332506-chr12:56359675..56362006,3	MCF-7	breast:
16	chr12:56318129..56322590-chr12:56359033..56362321,5	K562	blood:
17	chr12:56359758..56363158-chr12:56433727..56437301,5	K562	blood:

Variant related genes	Relation type
CDK2	TF binding region
PMEL	TF binding region
ENSG00000257449	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000136450	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000135482	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11171705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11550558	0.90[GIH][hapmap]
rs12307952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12309895	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17118206	1.00[CHD][hapmap];0.90[GIH][hapmap]
rs17118208	1.00[CHD][hapmap];0.90[GIH][hapmap]
rs2069398	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs3213122	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2069391	PMEL	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56346600-56360000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:56347200-56360000	Weak transcription	HSMMtube	muscle
3	chr12:56348200-56360000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:56358000-56363200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:56358600-56361200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:56358800-56361800	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr12:56359000-56360200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:56359000-56361400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:56359000-56361400	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr12:56359000-56361600	Active TSS	H9 Cell Line	embryonic stem cell
11	chr12:56359200-56360000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:56359200-56360200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr12:56359200-56360400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
14	chr12:56359200-56360400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:56359200-56360400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr12:56359200-56361400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:56359200-56361600	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr12:56359400-56360000	Enhancers	Primary B cells from peripheral blood	blood
19	chr12:56359400-56360000	Enhancers	Adipose Nuclei	Adipose
20	chr12:56359400-56360000	Enhancers	Brain Anterior Caudate	brain
21	chr12:56359400-56360000	Enhancers	Fetal Kidney	kidney
22	chr12:56359400-56360000	Enhancers	Placenta	Placenta
23	chr12:56359400-56360000	Enhancers	Fetal Stomach	stomach
24	chr12:56359400-56360000	Enhancers	Ovary	ovary
25	chr12:56359400-56360000	Enhancers	Placenta Amnion	Placenta Amnion
26	chr12:56359400-56360000	Enhancers	Dnd41	blood
27	chr12:56359400-56360200	Enhancers	Fetal Heart	heart
28	chr12:56359400-56361400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr12:56359600-56360000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:56359600-56360000	Enhancers	Primary T cells fromperipheralblood	blood
31	chr12:56359600-56360000	Enhancers	Primary hematopoietic stem cells	blood
32	chr12:56359600-56360000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr12:56359600-56360000	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr12:56359600-56360000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:56359600-56360000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:56359600-56360000	Enhancers	Brain Substantia Nigra	brain
37	chr12:56359600-56360000	Enhancers	Esophagus	oesophagus
38	chr12:56359600-56360000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr12:56359600-56360000	Enhancers	Fetal Muscle Leg	muscle
40	chr12:56359600-56360000	Enhancers	Fetal Thymus	thymus
41	chr12:56359600-56360000	Enhancers	Right Ventricle	heart
42	chr12:56359600-56360000	Enhancers	Thymus	Thymus
43	chr12:56359600-56360000	Enhancers	Spleen	Spleen
44	chr12:56359600-56360000	Enhancers	HMEC	breast
45	chr12:56359600-56360000	Enhancers	NHEK	skin
46	chr12:56359600-56360200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:56359600-56360200	Enhancers	Gastric	stomach
48	chr12:56359600-56360200	Enhancers	Pancreas	Pancrea
49	chr12:56359600-56360200	Enhancers	Small Intestine	intestine
50	chr12:56359600-56360200	Flanking Active TSS	Stomach Mucosa	stomach

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