Variant report

Variant	rs4759276
Chromosome Location	chr12:57526646-57526647
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	SPI1	chr12:57526606-57526968	HL-60	blood:	n/a	chr12:57526738-57526751 chr12:57526740-57526749 chr12:57526739-57526752 chr12:57526741-57526748 chr12:57526739-57526752
2	MAZ	chr12:57525540-57528414	IMR90	lung:	n/a	n/a
3	RCOR1	chr12:57526149-57527414	IMR90	lung:	n/a	n/a
4	POLR2A	chr12:57526174-57527232	U87	brain:	n/a	n/a
5	SPI1	chr12:57526562-57526850	K562	blood:	n/a	chr12:57526738-57526751 chr12:57526740-57526749 chr12:57526739-57526752 chr12:57526741-57526748 chr12:57526739-57526752
6	SPI1	chr12:57526585-57526860	K562	blood:	n/a	chr12:57526738-57526751 chr12:57526740-57526749 chr12:57526739-57526752 chr12:57526741-57526748 chr12:57526739-57526752
7	POLR2A	chr12:57526180-57527253	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57520108..57523293-chr12:57525745..57528597,4	MCF-7	breast:
2	chr12:57520290..57524994-chr12:57525334..57528665,7	K562	blood:
3	chr12:57521171..57523110-chr12:57526141..57527809,2	MCF-7	breast:
4	chr12:57525779..57529405-chr12:57538402..57541799,3	MCF-7	breast:
5	chr12:57526158..57527957-chr12:57535916..57537889,2	MCF-7	breast:

Variant related genes	Relation type
STAT6	TF binding region
ENSG00000259125	Chromatin interaction
ENSG00000166888	Chromatin interaction
ENSG00000123384	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10467124	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10876963	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11172106	0.80[CHB][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11172110	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11172111	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172113	0.84[CEU][hapmap];0.83[MEX][hapmap];0.85[EUR][1000 genomes]
rs12298170	0.80[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12309413	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12312693	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12322902	0.80[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12368672	0.81[CHD][hapmap];0.88[GIH][hapmap]
rs324013	0.89[GIH][hapmap];0.96[MEX][hapmap]
rs4759275	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4759276	SMARCC2	cis	cerebellum	SCAN
rs4759276	ATP5B	cis	cerebellum	SCAN
rs4759276	STAT6	cis	parietal	SCAN
rs4759276	KIF5A	cis	cerebellum	SCAN
rs4759276	KRT82	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57523000-57530400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:57523400-57557200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:57523600-57528200	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr12:57523600-57529600	Enhancers	A549	lung
5	chr12:57523600-57532400	Weak transcription	Pancreas	Pancrea
6	chr12:57523800-57527000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr12:57523800-57527200	Flanking Active TSS	Brain Hippocampus Middle	brain
8	chr12:57523800-57527400	Flanking Active TSS	NH-A	brain
9	chr12:57523800-57529600	Enhancers	Stomach Mucosa	stomach
10	chr12:57523800-57530000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:57523800-57530600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr12:57523800-57532600	Weak transcription	Gastric	stomach
13	chr12:57523800-57537000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr12:57524000-57527400	Enhancers	Aorta	Aorta
15	chr12:57524000-57528200	Enhancers	H1 Cell Line	embryonic stem cell
16	chr12:57524000-57530400	Enhancers	H9 Cell Line	embryonic stem cell
17	chr12:57524000-57530400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:57524000-57542200	Weak transcription	HMEC	breast
19	chr12:57524000-57543000	Weak transcription	NHEK	skin
20	chr12:57524200-57526800	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr12:57524400-57527200	Flanking Active TSS	NHDF-Ad	bronchial
22	chr12:57524400-57529200	Genic enhancers	Fetal Stomach	stomach
23	chr12:57524400-57530000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr12:57524600-57529400	Enhancers	Placenta	Placenta
25	chr12:57524600-57530400	Enhancers	Left Ventricle	heart
26	chr12:57524800-57526800	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
27	chr12:57524800-57527000	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr12:57524800-57527000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr12:57524800-57527000	Enhancers	Spleen	Spleen
30	chr12:57524800-57527200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:57524800-57527200	Flanking Active TSS	Brain Anterior Caudate	brain
32	chr12:57524800-57530600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr12:57524800-57530800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:57525000-57526800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:57525000-57526800	Transcr. at gene 5' and 3'	HSMM	muscle
36	chr12:57525000-57526800	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
37	chr12:57525000-57527800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr12:57525200-57526800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:57525200-57527000	Flanking Active TSS	Rectal Smooth Muscle	rectum
40	chr12:57525200-57529400	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr12:57525200-57529800	Enhancers	Duodenum Mucosa	Duodenum
42	chr12:57525400-57529400	Genic enhancers	Fetal Intestine Small	intestine
43	chr12:57525600-57527000	Flanking Active TSS	Colon Smooth Muscle	Colon
44	chr12:57525600-57527000	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
45	chr12:57525600-57528200	Enhancers	Fetal Heart	heart
46	chr12:57525800-57526800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:57525800-57526800	Flanking Active TSS	Right Atrium	heart
48	chr12:57525800-57527000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr12:57525800-57527000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr12:57525800-57527200	Genic enhancers	Fetal Intestine Large	intestine

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