Variant report

Variant	rs12816499
Chromosome Location	chr12:122708077-122708078
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:122707988-122708660	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:122708000-122708530	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr12:122708062-122708277	H1-hESC	embryonic stem cell:	n/a	n/a
4	IRF1	chr12:122708075-122708395	K562	blood:	n/a	n/a
5	TEAD4	chr12:122707902-122708409	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr12:122708050-122708307	H1-hESC	embryonic stem cell:	n/a	n/a
7	TEAD4	chr12:122707912-122708464	K562	blood:	n/a	n/a
8	TEAD4	chr12:122707998-122708389	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr12:122707999-122708369	H1-hESC	embryonic stem cell:	n/a	n/a
10	MYC	chr12:122708077-122708375	K562	blood:	n/a	n/a
11	POLR2A	chr12:122707850-122708653	K562	blood:	n/a	n/a
12	NR2F2	chr12:122707988-122708627	K562	blood:	n/a	n/a
13	POLR2A	chr12:122708032-122708658	K562	blood:	n/a	n/a
14	ATF1	chr12:122708049-122708529	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122698849..122704062-chr12:122705218..122711671,13	MCF-7	breast:
2	chr12:122687145..122691347-chr12:122704062..122708275,6	MCF-7	breast:
3	chr12:122707574..122711015-chr12:122711233..122714440,3	K562	blood:
4	chr12:122705056..122708320-chr12:122708578..122712255,7	MCF-7	breast:
5	chr12:122689976..122691920-chr12:122706553..122708365,2	MCF-7	breast:
6	chr12:122706789..122708655-chr12:122709178..122711069,2	K562	blood:
7	chr12:122707649..122712350-chr12:122748538..122752681,8	K562	blood:
8	chr12:122685663..122693033-chr12:122702446..122708793,8	K562	blood:

No data

Variant related genes	Relation type
DIABLO	TF binding region
ENSG00000184047	Chromatin interaction
ENSG00000256861	Chromatin interaction
ENSG00000139719	Chromatin interaction
ENSG00000176383	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10270	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs10848035	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11060167	0.95[CEU][hapmap];0.85[YRI][hapmap];0.88[EUR][1000 genomes]
rs11060333	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs12423987	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs12424872	0.84[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12425684	0.84[EUR][1000 genomes]
rs12578739	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12578815	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12578863	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12580084	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs12809220	0.87[EUR][1000 genomes]
rs12810587	0.91[CEU][hapmap]
rs12811503	0.87[EUR][1000 genomes]
rs12814516	0.89[EUR][1000 genomes]
rs12814554	0.82[EUR][1000 genomes]
rs12814923	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs12816400	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12820704	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12822121	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs12824385	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12824701	0.91[CEU][hapmap];0.85[JPT][hapmap]
rs12824925	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs12825008	0.88[EUR][1000 genomes]
rs12825149	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs12825279	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12826834	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12827843	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12831210	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1512023	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs1967291	0.86[EUR][1000 genomes]
rs2063510	0.85[JPT][hapmap]
rs2068223	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271408	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2271409	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2277332	0.84[JPT][hapmap]
rs2277333	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34383196	0.88[EUR][1000 genomes]
rs35030971	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35772530	0.89[EUR][1000 genomes]
rs35963777	0.84[EUR][1000 genomes]
rs3782153	0.80[EUR][1000 genomes]
rs3782154	0.85[JPT][hapmap]
rs3809116	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4567503	0.85[JPT][hapmap]
rs4758649	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4758650	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs4758670	0.84[JPT][hapmap]
rs4758677	0.95[CEU][hapmap];0.85[YRI][hapmap];0.88[EUR][1000 genomes]
rs6488906	0.86[EUR][1000 genomes]
rs6488909	0.85[EUR][1000 genomes]
rs7388	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7962385	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs7963565	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs7970027	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs872451	0.91[CEU][hapmap]
rs907482	0.83[CEU][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12816499	VPS33A	cis	multi-tissue	Pritchard
rs12816499	MLXIP	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122689000-122709000	Weak transcription	Right Atrium	heart
2	chr12:122690800-122708400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:122690800-122708800	Strong transcription	Fetal Brain Female	brain
4	chr12:122690800-122709400	Weak transcription	Stomach Mucosa	stomach
5	chr12:122691000-122708200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr12:122691000-122708800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:122691000-122708800	Strong transcription	A549	lung
8	chr12:122691200-122708400	Strong transcription	Duodenum Mucosa	Duodenum
9	chr12:122691200-122708600	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr12:122691200-122708800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:122691200-122709000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:122691200-122709200	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr12:122691400-122708200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr12:122691400-122708400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr12:122691400-122708400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:122691400-122708800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr12:122691400-122709000	Strong transcription	Primary B cells from peripheral blood	blood
18	chr12:122691400-122709000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr12:122691400-122709000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:122691400-122709000	Strong transcription	Fetal Thymus	thymus
21	chr12:122691600-122708400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:122691600-122708400	Strong transcription	Placenta	Placenta
23	chr12:122691600-122708400	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr12:122691600-122709000	Strong transcription	Brain Hippocampus Middle	brain
25	chr12:122691600-122709000	Strong transcription	Fetal Muscle Leg	muscle
26	chr12:122691600-122709200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:122691800-122708400	Strong transcription	Liver	Liver
28	chr12:122691800-122708600	Strong transcription	Rectal Smooth Muscle	rectum
29	chr12:122691800-122709000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:122691800-122709000	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr12:122692000-122708400	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr12:122692200-122708400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr12:122692200-122709200	Strong transcription	Fetal Muscle Trunk	muscle
34	chr12:122692400-122709200	Strong transcription	Fetal Lung	lung
35	chr12:122692600-122709000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:122695200-122708200	Strong transcription	Lung	lung
37	chr12:122695400-122709000	Strong transcription	Primary T cells from cord blood	blood
38	chr12:122697000-122708400	Strong transcription	Ovary	ovary
39	chr12:122697200-122708400	Strong transcription	Fetal Stomach	stomach
40	chr12:122697200-122709000	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr12:122697600-122708400	Strong transcription	Left Ventricle	heart
42	chr12:122700400-122708400	Weak transcription	Pancreas	Pancrea
43	chr12:122700600-122709200	Weak transcription	Small Intestine	intestine
44	chr12:122700800-122708400	Weak transcription	Fetal Heart	heart
45	chr12:122701600-122708200	Strong transcription	Fetal Intestine Small	intestine
46	chr12:122703000-122708600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr12:122703600-122708800	Strong transcription	NHEK	skin
48	chr12:122704600-122709000	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr12:122704600-122709000	Strong transcription	Fetal Intestine Large	intestine
50	chr12:122704800-122708200	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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