Variant report

Variant	rs11599546
Chromosome Location	chr10:96995687-96995688
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	SP1	chr10:96995534-96996414	HCT-116	colon:	n/a	n/a
2	FOSL2	chr10:96995668-96996288	SK-N-SH	brain:	n/a	chr10:96995982-96995990 chr10:96995980-96995992 chr10:96995924-96995933 chr10:96995872-96995881 chr10:96995924-96995931 chr10:96995924-96995932
3	POLR2A	chr10:96995624-96996721	GM12878	blood:	n/a	n/a
4	BCL3	chr10:96995658-96996450	GM12878	blood:	n/a	chr10:96996172-96996181 chr10:96995923-96995932 chr10:96995981-96995990 chr10:96995924-96995933
5	POLR2A	chr10:96995646-96996730	HepG2	liver:	n/a	n/a
6	POLR2A	chr10:96995685-96996146	U87	brain:	n/a	n/a
7	POLR2A	chr10:96995683-96996202	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr10:96995526-96995694	K562	blood:	n/a	n/a
9	CBX3	chr10:96995675-96996459	HCT-116	colon:	n/a	n/a
10	POLR2A	chr10:96995314-96996890	GM12892	blood:	n/a	n/a
11	JUN	chr10:96995623-96996789	K562	blood:	n/a	chr10:96995982-96995990 chr10:96995980-96995992 chr10:96996311-96996323 chr10:96995924-96995933 chr10:96995872-96995881 chr10:96995924-96995931 chr10:96995924-96995932
12	CEBPB	chr10:96995616-96996574	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr10:96995680-96996150	PANC-1	pancreas:	n/a	n/a
14	GATA3	chr10:96995518-96996758	SK-N-SH	brain:	n/a	chr10:96995983-96995992 chr10:96995731-96995741
15	POLR2A	chr10:96995520-96996885	GM12891	blood:	n/a	n/a
16	CEBPB	chr10:96995615-96996258	HCT-116	colon:	n/a	n/a
17	JUND	chr10:96995531-96996743	SK-N-SH	brain:	n/a	chr10:96995982-96995990 chr10:96995980-96995992 chr10:96996311-96996323 chr10:96995924-96995933 chr10:96995872-96995881 chr10:96995922-96995933 chr10:96995924-96995931 chr10:96995924-96995932
18	BCLAF1	chr10:96995638-96996727	GM12878	blood:	n/a	chr10:96996172-96996181 chr10:96995923-96995932 chr10:96995981-96995990 chr10:96995924-96995933
19	STAT1	chr10:96995543-96996717	Hela-S3	cervix:	n/a	chr10:96996170-96996181 chr10:96996026-96996040 chr10:96995923-96995932 chr10:96995924-96995933
20	POLR2A	chr10:96995480-96996709	K562	blood:	n/a	n/a
21	NFIC	chr10:96995589-96996710	GM12878	blood:	n/a	n/a
22	RXRA	chr10:96995680-96996762	SK-N-SH	brain:	n/a	chr10:96995739-96995746 chr10:96996172-96996181 chr10:96996322-96996335 chr10:96995924-96995933 chr10:96996322-96996335 chr10:96996323-96996334
23	NFIC	chr10:96995651-96996607	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr10:96995430-96996827	GM12891	blood:	n/a	n/a
25	ATF3	chr10:96995671-96995931	K562	blood:	n/a	n/a
26	TCF7L2	chr10:96995624-96996211	PANC-1	pancreas:	n/a	chr10:96995924-96995933
27	CEBPB	chr10:96995578-96996607	GM12878	blood:	n/a	n/a
28	FOSL1	chr10:96995525-96996783	HCT-116	colon:	n/a	chr10:96995982-96995990 chr10:96995980-96995992 chr10:96996311-96996323 chr10:96995924-96995933 chr10:96995872-96995881 chr10:96995924-96995931 chr10:96995924-96995932
29	TCF12	chr10:96995559-96996796	SK-N-SH	brain:	n/a	n/a
30	EP300	chr10:96995593-96996483	SK-N-SH	brain:	n/a	chr10:96996172-96996186 chr10:96996118-96996132 chr10:96995924-96995933
31	POLR2A	chr10:96995533-96996701	GM12878	blood:	n/a	n/a
32	NFATC1	chr10:96995598-96996710	GM12878	blood:	n/a	n/a
33	PBX3	chr10:96995546-96996510	SK-N-SH	brain:	n/a	n/a
34	PBX3	chr10:96995545-96996180	SK-N-SH	brain:	n/a	n/a
35	GATA3	chr10:96995575-96996769	SK-N-SH	brain:	n/a	chr10:96995983-96995992 chr10:96995731-96995741
36	POLR2A	chr10:96995565-96996786	A549	lung:	n/a	n/a
37	TCF12	chr10:96995563-96996463	SK-N-SH	brain:	n/a	n/a
38	JUND	chr10:96995446-96996723	SK-N-SH	brain:	n/a	chr10:96995982-96995990 chr10:96995980-96995992 chr10:96996311-96996323 chr10:96995924-96995933 chr10:96995872-96995881 chr10:96995922-96995933 chr10:96995924-96995931 chr10:96995924-96995932
39	POLR2A	chr10:96995440-96996805	GM12892	blood:	n/a	n/a
40	FOS	chr10:96995586-96996233	HUVEC	blood vessel:	n/a	chr10:96995982-96995990 chr10:96995980-96995992 chr10:96995980-96995991 chr10:96995924-96995933 chr10:96995872-96995881 chr10:96995924-96995931 chr10:96995924-96995932
41	MAX	chr10:96995605-96996381	HCT-116	colon:	n/a	chr10:96995923-96995932 chr10:96995924-96995933 chr10:96995981-96995990
42	FOXM1	chr10:96995667-96996620	GM12878	blood:	n/a	n/a
43	POLR2A	chr10:96995686-96996647	K562	blood:	n/a	n/a
44	MTA3	chr10:96995454-96996831	GM12878	blood:	n/a	n/a
45	NFATC1	chr10:96995604-96996648	GM12878	blood:	n/a	n/a
46	ATF2	chr10:96995637-96996580	GM12878	blood:	n/a	n/a
47	POLR2A	chr10:96995431-96996803	GM12892	blood:	n/a	n/a
48	TCF7L2	chr10:96995596-96996130	Hela-S3	cervix:	n/a	chr10:96995924-96995933
49	PRDM1	chr10:96995656-96996135	Hela-S3	cervix:	n/a	chr10:96995924-96995933 chr10:96995904-96995913
50	FOSL1	chr10:96995544-96996305	HCT-116	colon:	n/a	chr10:96995982-96995990 chr10:96995980-96995992 chr10:96995924-96995933 chr10:96995872-96995881 chr10:96995924-96995931 chr10:96995924-96995932

Variant related genes	Relation type
ENSG00000234026	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10882570	1.00[ASN][1000 genomes]
rs10882571	1.00[ASN][1000 genomes]
rs11188236	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11188238	0.92[ASN][1000 genomes]
rs11188239	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188240	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11598953	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11598991	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11872	0.82[ASN][1000 genomes]
rs12262534	0.97[ASN][1000 genomes]
rs12783947	0.92[ASN][1000 genomes]
rs12784385	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3210020	0.82[ASN][1000 genomes]
rs45510800	0.82[ASN][1000 genomes]
rs45605435	0.82[ASN][1000 genomes]
rs7909072	0.95[ASN][1000 genomes]
rs7924214	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv21432	chr10:96856006-96996043	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv15160	chr10:96942869-97074756	Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers 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 target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96990000-96995800	Weak transcription	HepG2	liver
2	chr10:96990800-96997400	Weak transcription	Stomach Mucosa	stomach
3	chr10:96990800-97005200	Weak transcription	Psoas Muscle	Psoas
4	chr10:96991000-96995800	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr10:96991000-96996000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr10:96991000-96996200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr10:96991000-96996400	Weak transcription	Right Ventricle	heart
8	chr10:96991000-96997200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr10:96991000-96997400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr10:96991000-96997600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr10:96991000-96999800	Weak transcription	Fetal Lung	lung
12	chr10:96991000-97001200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr10:96991000-97001600	Weak transcription	Thymus	Thymus
14	chr10:96991000-97006400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr10:96991000-97006400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr10:96991000-97006600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr10:96991000-97006600	Weak transcription	Colon Smooth Muscle	Colon
18	chr10:96991000-97006600	Weak transcription	Right Atrium	heart
19	chr10:96991000-97007600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr10:96991000-97020400	Weak transcription	Fetal Muscle Leg	muscle
21	chr10:96991000-97024000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr10:96991200-96996400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr10:96991200-97000000	Weak transcription	Fetal Kidney	kidney
24	chr10:96991200-97000200	Weak transcription	Fetal Thymus	thymus
25	chr10:96991400-97019000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr10:96991600-96996200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr10:96991600-96997400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr10:96991600-97001000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr10:96992000-97005000	Strong transcription	Duodenum Mucosa	Duodenum
30	chr10:96992000-97005800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr10:96992200-96997400	Weak transcription	Small Intestine	intestine
32	chr10:96992200-97009000	Strong transcription	Liver	Liver
33	chr10:96992400-96996000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr10:96992400-96996200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr10:96992400-96996200	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr10:96992400-96998600	Strong transcription	Fetal Stomach	stomach
37	chr10:96992400-96998800	Strong transcription	Left Ventricle	heart
38	chr10:96992400-96999000	Strong transcription	Adipose Nuclei	Adipose
39	chr10:96992400-97000000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr10:96992400-97006200	Strong transcription	Placenta Amnion	Placenta Amnion
41	chr10:96992600-96998600	Strong transcription	Lung	lung
42	chr10:96992600-97004000	Strong transcription	Fetal Intestine Large	intestine
43	chr10:96993000-96996600	Enhancers	NHDF-Ad	bronchial
44	chr10:96993000-96996800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr10:96993200-96998800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr10:96993800-96996200	Weak transcription	Esophagus	oesophagus
47	chr10:96994000-96996200	Weak transcription	Aorta	Aorta
48	chr10:96994200-96996200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr10:96994200-96997400	Weak transcription	Pancreas	Pancrea
50	chr10:96994600-96996000	Enhancers	Osteobl	bone

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