Variant report

Variant	rs752471
Chromosome Location	chr12:105606670-105606671
allele	A/G
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	chr12:105605998-105606786	HepG2	liver:	n/a	n/a
2	FOS	chr12:105606221-105606683	MCF10A-Er-Src	breast:	n/a	chr12:105606451-105606461
3	STAT3	chr12:105606230-105606694	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr12:105606195-105606874	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr12:105606355-105606702	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr12:105606438-105606679	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:105606486..105608815-chr12:105609324..105611383,2	K562	blood:
2	chr12:105605767..105607700-chr12:105638996..105640802,2	MCF-7	breast:
3	chr12:105602998..105604968-chr12:105605214..105607629,2	MCF-7	breast:

Variant related genes	Relation type
APPL2	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1107756	0.82[CHB][hapmap]
rs1196751	0.86[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1196752	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1196758	0.85[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1196761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196830	0.80[ASN][1000 genomes]
rs1196845	0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs1196865	0.96[CEU][hapmap];0.83[TSI][hapmap]
rs2246510	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2440695	0.82[CHB][hapmap]
rs2464184	0.82[CHB][hapmap]
rs6539185	0.84[CHD][hapmap]
rs750060	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7954946	0.85[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap]
rs880797	0.81[CHB][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	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv455704	chr12:105583877-105651356	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
3	nsv560053	chr12:105583877-105651356	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS 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	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs752471	APPL2	cis	cerebellum	SCAN
rs752471	ALDH1L2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105546800-105625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:105558800-105615200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:105571400-105617800	Weak transcription	K562	blood
4	chr12:105577000-105607200	Strong transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:105577400-105616200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:105577800-105607400	Strong transcription	Duodenum Mucosa	Duodenum
7	chr12:105578000-105607400	Strong transcription	Fetal Brain Female	brain
8	chr12:105578000-105623200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr12:105578200-105620000	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr12:105579000-105612400	Strong transcription	Stomach Smooth Muscle	stomach
11	chr12:105580200-105613200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:105584000-105627000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr12:105587400-105609000	Weak transcription	Fetal Brain Male	brain
14	chr12:105589200-105612200	Weak transcription	Psoas Muscle	Psoas
15	chr12:105589400-105608600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:105589400-105612400	Weak transcription	Fetal Heart	heart
17	chr12:105590200-105620000	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr12:105590400-105618800	Strong transcription	Primary B cells from peripheral blood	blood
19	chr12:105591000-105619400	Strong transcription	Primary T cells from cord blood	blood
20	chr12:105594400-105614400	Weak transcription	Small Intestine	intestine
21	chr12:105594600-105607200	Strong transcription	Fetal Intestine Large	intestine
22	chr12:105594600-105607600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:105595000-105612800	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:105595000-105618800	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr12:105595200-105607800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr12:105595600-105612800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:105595800-105612000	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr12:105595800-105612200	Weak transcription	Right Atrium	heart
29	chr12:105595800-105616600	Strong transcription	Primary hematopoietic stem cells	blood
30	chr12:105596000-105617000	Strong transcription	Fetal Lung	lung
31	chr12:105596400-105621800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:105596600-105607600	Strong transcription	Liver	Liver
33	chr12:105597200-105607800	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr12:105599400-105612400	Strong transcription	Brain Anterior Caudate	brain
35	chr12:105599800-105607200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:105599800-105610800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr12:105600600-105607000	Weak transcription	Stomach Mucosa	stomach
38	chr12:105600600-105608600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr12:105600800-105610000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr12:105600800-105626800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:105601000-105612400	Strong transcription	Fetal Stomach	stomach
42	chr12:105601000-105615800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:105601000-105619200	Weak transcription	GM12878-XiMat	blood
44	chr12:105601200-105610200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr12:105601200-105610400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr12:105601400-105610400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr12:105601400-105615800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr12:105601600-105608400	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr12:105602000-105608000	Weak transcription	HepG2	liver
50	chr12:105602000-105608400	Weak transcription	Colon Smooth Muscle	Colon

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