Variant report

Variant	rs12574259
Chromosome Location	chr11:46704439-46704440
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr11:46704322-46704512	HepG2	liver:	n/a	n/a
2	ZNF143	chr11:46704370-46704599	Hela-S3	cervix:	n/a	n/a
3	STAT3	chr11:46704293-46704493	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr11:46704303-46704583	Hela-S3	cervix:	n/a	n/a
5	ZNF143	chr11:46704398-46704572	H1-hESC	embryonic stem cell:	n/a	n/a
6	RCOR1	chr11:46704380-46704617	K562	blood:	n/a	n/a
7	ZNF143	chr11:46704383-46704671	K562	blood:	n/a	n/a
8	MAFK	chr11:46704245-46704516	HepG2	liver:	n/a	n/a
9	ZNF143	chr11:46704425-46704559	GM12878	blood:	n/a	n/a
10	POLR2A	chr11:46704365-46704574	HepG2	liver:	n/a	n/a
11	MAFF	chr11:46704271-46704498	HepG2	liver:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:46704275..46710507-chr11:46714249..46719303,8	MCF-7	breast:
2	chr11:46704037..46706456-chr11:46719312..46722253,3	K562	blood:
3	chr11:46208238..46210812-chr11:46703843..46706732,2	K562	blood:

No data

Variant related genes	Relation type
ARHGAP1	TF binding region
ENSG00000175220	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10160701	0.93[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap]
rs10769204	0.81[JPT][hapmap]
rs10838610	0.81[JPT][hapmap]
rs10838613	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[EUR][1000 genomes]
rs11038906	0.93[CEU][hapmap]
rs11038910	0.81[JPT][hapmap]
rs11038914	0.93[CEU][hapmap];0.92[TSI][hapmap]
rs11038919	0.93[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs11038974	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11819869	0.93[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap]
rs12272795	0.93[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs12292425	0.93[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs12295266	0.82[EUR][1000 genomes]
rs12573978	0.93[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap]
rs12574918	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12577603	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12578042	0.93[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap]
rs1489192	0.93[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap]
rs17197116	0.91[LWK][hapmap];0.88[MKK][hapmap]
rs17787804	0.81[JPT][hapmap]
rs28372918	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2902858	0.93[CEU][hapmap];0.82[GIH][hapmap];0.95[TSI][hapmap]
rs3136435	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3136456	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3136474	0.83[ASN][1000 genomes]
rs3136490	0.81[ASN][1000 genomes]
rs35623865	0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs3802888	0.93[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap]
rs3802890	0.81[JPT][hapmap]
rs4307676	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4319473	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][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];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4423142	0.93[EUR][1000 genomes]
rs55657382	0.84[EUR][1000 genomes]
rs55661562	0.84[EUR][1000 genomes]
rs55896955	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56349329	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57739486	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57744667	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60722866	0.83[EUR][1000 genomes]
rs60932698	0.85[EUR][1000 genomes]
rs61882756	0.80[EUR][1000 genomes]
rs61882757	0.82[EUR][1000 genomes]
rs61882758	0.82[EUR][1000 genomes]
rs61884264	0.82[EUR][1000 genomes]
rs61884271	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs61884273	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs61884274	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs61884292	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61884295	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61884301	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6485685	0.84[EUR][1000 genomes]
rs6485686	0.81[JPT][hapmap]
rs7108770	0.84[EUR][1000 genomes]
rs7109698	0.93[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs7112229	0.85[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap]
rs7122039	0.93[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs7125907	0.93[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs7126316	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7126343	0.87[EUR][1000 genomes]
rs7127529	0.93[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap]
rs7128092	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73449983	0.82[EUR][1000 genomes]
rs7481312	0.93[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.80[EUR][1000 genomes]
rs7484002	0.93[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs7924401	0.83[EUR][1000 genomes]
rs7925678	0.81[JPT][hapmap]
rs7926389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7932866	0.93[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs7949282	0.81[JPT][hapmap]
rs7949371	0.81[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	nsv1044225	chr11:46472580-46771102	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv541030	chr11:46472580-46771102	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12574259	ATG13	cis	parietal	SCAN
rs12574259	PROX1	trans	cerebellum	SCAN
rs12574259	DKFZp779M0652	cis	parietal	SCAN
rs12574259	C11orf49	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46667200-46717000	Strong transcription	Brain Germinal Matrix	brain
2	chr11:46689600-46706200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr11:46691600-46705600	Weak transcription	Fetal Brain Male	brain
4	chr11:46691600-46709200	Weak transcription	HUVEC	blood vessel
5	chr11:46697200-46705200	Strong transcription	Fetal Brain Female	brain
6	chr11:46697200-46705800	Strong transcription	Thymus	Thymus
7	chr11:46697200-46716000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr11:46697200-46721200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:46697800-46704800	Weak transcription	Fetal Heart	heart
10	chr11:46697800-46706200	Strong transcription	Rectal Smooth Muscle	rectum
11	chr11:46697800-46709200	Strong transcription	Fetal Stomach	stomach
12	chr11:46698000-46708800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr11:46698000-46708800	Strong transcription	Stomach Smooth Muscle	stomach
14	chr11:46698000-46718600	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr11:46698200-46705600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr11:46698200-46706000	Strong transcription	Fetal Lung	lung
17	chr11:46698200-46706200	Strong transcription	Dnd41	blood
18	chr11:46698200-46708600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr11:46698400-46709000	Weak transcription	Fetal Kidney	kidney
20	chr11:46698400-46719400	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr11:46698600-46704600	Strong transcription	HepG2	liver
22	chr11:46698600-46704800	Strong transcription	HSMM	muscle
23	chr11:46698600-46705000	Strong transcription	Brain Inferior Temporal Lobe	brain
24	chr11:46698600-46705800	Strong transcription	Gastric	stomach
25	chr11:46698600-46706600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr11:46698800-46705000	Strong transcription	Brain Cingulate Gyrus	brain
27	chr11:46698800-46706200	Strong transcription	Fetal Thymus	thymus
28	chr11:46699000-46704800	Strong transcription	Brain Hippocampus Middle	brain
29	chr11:46699000-46704800	Strong transcription	Brain Substantia Nigra	brain
30	chr11:46699000-46704800	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr11:46699000-46705000	Strong transcription	Fetal Muscle Trunk	muscle
32	chr11:46699000-46705000	Weak transcription	Right Atrium	heart
33	chr11:46699000-46706000	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr11:46699000-46706000	Strong transcription	Lung	lung
35	chr11:46699200-46705600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr11:46699200-46706000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr11:46699200-46706000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr11:46699200-46706200	Strong transcription	Primary T cells from cord blood	blood
39	chr11:46699200-46706200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr11:46699200-46706200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr11:46699200-46706400	Strong transcription	Primary B cells from cord blood	blood
42	chr11:46699200-46715800	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr11:46699200-46716400	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr11:46699200-46717000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr11:46699200-46717200	Strong transcription	Liver	Liver
46	chr11:46699200-46719000	Strong transcription	Primary B cells from peripheral blood	blood
47	chr11:46699400-46705000	Strong transcription	Colonic Mucosa	Colon
48	chr11:46699600-46705200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr11:46699600-46706600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr11:46699800-46704600	Strong transcription	Primary T helper naive cells from peripheral blood	blood

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