Variant report

Variant	rs899653
Chromosome Location	chr12:57883801-57883802
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr12:57881281-57883804	K562	blood:	n/a	chr12:57882014-57882023 chr12:57882152-57882161 chr12:57883182-57883190 chr12:57882015-57882024
2	POLR2A	chr12:57883605-57883915	K562	blood:	n/a	n/a
3	POLR2A	chr12:57883565-57884475	H1-hESC	embryonic stem cell:	n/a	n/a
4	WRNIP1	chr12:57883778-57883880	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:57883627-57884061	HCT-116	colon:	n/a	n/a
6	POLR2A	chr12:57883719-57884237	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57879869..57888452-chr12:57905809..57918310,36	K562	blood:
2	chr12:57872773..57878513-chr12:57879040..57886839,8	K562	blood:
3	chr12:57855242..57858206-chr12:57882251..57883801,2	K562	blood:
4	chr12:57881812..57883506-chr12:57883625..57886800,4	MCF-7	breast:
5	chr12:57880356..57884964-chr12:57910434..57915758,10	MCF-7	breast:
6	chr12:57882180..57883907-chr12:57905478..57906996,2	MCF-7	breast:
7	chr12:57854130..57857750-chr12:57881459..57884101,5	K562	blood:
8	chr12:57881044..57886958-chr12:57910925..57918058,16	MCF-7	breast:
9	chr12:57869556..57871935-chr12:57881103..57884583,3	K562	blood:
10	chr12:57848182..57850484-chr12:57880307..57884604,3	K562	blood:
11	chr12:57883464..57886138-chr12:57902032..57904531,3	K562	blood:
12	chr12:57881482..57885096-chr12:57938469..57941069,3	K562	blood:
13	chr12:57879207..57888227-chr12:57906247..57918451,36	K562	blood:

No data

Variant related genes	Relation type
ARHGAP9	TF binding region
ENSG00000166987	Chromatin interaction
ENSG00000139269	Chromatin interaction
ENSG00000111087	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000123329	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000175203	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000264046	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1148555	0.95[CHD][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap]
rs1148557	0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.80[ASN][1000 genomes]
rs1284605	0.95[CHD][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap]
rs1284606	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1299737	0.86[ASN][1000 genomes]
rs1617196	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1669294	0.83[ASN][1000 genomes]
rs1669296	0.95[CHD][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap]
rs1678537	0.83[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap]
rs1709871	0.83[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap]
rs1709874	0.90[ASN][1000 genomes]
rs2127318	1.00[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes]
rs2620679	0.82[CHB][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.96[TSI][hapmap]
rs2672571	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2928382	0.83[ASN][1000 genomes]
rs3847699	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs472895	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4760273	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs496245	0.83[CEU][hapmap]
rs508904	1.00[CEU][hapmap];0.81[CHB][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs511752	0.83[CEU][hapmap];0.85[CHB][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs539244	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs541869	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs542278	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs569251	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs697221	0.92[CHD][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap]
rs703835	0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs703837	0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs7485148	0.84[AFR][1000 genomes]
rs775241	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs775324	0.81[CHB][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.96[TSI][hapmap]
rs776038	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[ASN][1000 genomes]
rs776039	0.85[ASN][1000 genomes]
rs7964074	1.00[ASW][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap]
rs796546	0.90[ASN][1000 genomes]
rs7969683	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9737891	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers 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 miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
9	nsv469411	chr12:57844049-57921188	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
10	nsv559032	chr12:57844049-57921188	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
11	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
12	nsv899119	chr12:57851182-57923451	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers 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 lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
13	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
14	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
15	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs899653	AVIL	cis	cerebellum	SCAN
rs899653	ACVRL1	cis	cerebellum	SCAN
rs899653	KRT81	cis	parietal	SCAN
rs899653	CALCOCO1	cis	cerebellum	SCAN
rs899653	ITGB7	cis	cerebellum	SCAN
rs899653	STAT6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57882600-57884000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:57882600-57884200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr12:57882600-57884400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:57882800-57905800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:57883000-57884200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:57883000-57884200	Genic enhancers	Brain Cingulate Gyrus	brain
7	chr12:57883000-57884200	Genic enhancers	Lung	lung
8	chr12:57883000-57884800	Weak transcription	Fetal Heart	heart
9	chr12:57883000-57910600	Weak transcription	Right Atrium	heart
10	chr12:57883200-57884000	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
11	chr12:57883200-57884000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:57883200-57884000	Genic enhancers	Fetal Brain Female	brain
13	chr12:57883200-57884000	Weak transcription	Small Intestine	intestine
14	chr12:57883200-57884200	Genic enhancers	Gastric	stomach
15	chr12:57883200-57884400	Strong transcription	Psoas Muscle	Psoas
16	chr12:57883200-57885400	Strong transcription	Placenta Amnion	Placenta Amnion
17	chr12:57883200-57887000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
18	chr12:57883200-57887000	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr12:57883200-57887000	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr12:57883200-57887000	Strong transcription	Primary B cells from cord blood	blood
21	chr12:57883200-57887000	Strong transcription	Primary hematopoietic stem cells	blood
22	chr12:57883200-57887000	Strong transcription	Colonic Mucosa	Colon
23	chr12:57883200-57887000	Strong transcription	Fetal Intestine Large	intestine
24	chr12:57883200-57887000	Strong transcription	Fetal Lung	lung
25	chr12:57883200-57887000	Strong transcription	Placenta	Placenta
26	chr12:57883200-57890000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:57883200-57893600	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr12:57883200-57900600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:57883200-57900600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr12:57883200-57900800	Strong transcription	Thymus	Thymus
31	chr12:57883200-57902400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:57883200-57911200	Strong transcription	Fetal Intestine Small	intestine
33	chr12:57883400-57884000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
34	chr12:57883400-57884000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr12:57883400-57884000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:57883400-57884200	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:57883400-57884400	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:57883400-57885400	Strong transcription	Fetal Brain Male	brain
39	chr12:57883400-57885400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr12:57883400-57885800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr12:57883400-57885800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr12:57883400-57885800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:57883400-57885800	Strong transcription	Rectal Smooth Muscle	rectum
44	chr12:57883400-57885800	Strong transcription	HSMM	muscle
45	chr12:57883400-57886000	Strong transcription	Brain Germinal Matrix	brain
46	chr12:57883400-57886200	Weak transcription	Stomach Mucosa	stomach
47	chr12:57883400-57886600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:57883400-57886600	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr12:57883400-57886800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr12:57883400-57886800	Strong transcription	Brain Angular Gyrus	brain

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