Variant report

Variant	rs899010
Chromosome Location	chr11:10477127-10477128
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	chr11:10476180-10478518	IMR90	lung:	n/a	n/a
2	RCOR1	chr11:10476407-10478075	GM12878	blood:	n/a	n/a
3	RELA	chr11:10476067-10478371	GM12891	blood:	n/a	n/a
4	BHLHE40	chr11:10476353-10478392	K562	blood:	n/a	n/a
5	RELA	chr11:10476246-10478481	GM19099	blood:	n/a	n/a
6	E2F6	chr11:10476529-10478454	K562	blood:	n/a	chr11:10478174-10478183
7	TCF12	chr11:10476150-10477343	A549	lung:	n/a	n/a
8	MAX	chr11:10476252-10478118	A549	lung:	n/a	chr11:10476971-10476981 chr11:10476970-10476979
9	POLR2A	chr11:10476302-10478356	GM12878	blood:	n/a	n/a
10	JUN	chr11:10475959-10478519	K562	blood:	n/a	chr11:10476625-10476633 chr11:10476624-10476634 chr11:10477854-10477864 chr11:10476624-10476634 chr11:10478179-10478190 chr11:10477748-10477762
11	IRF1	chr11:10476981-10477861	K562	blood:	n/a	chr11:10477272-10477282
12	GATA1	chr11:10476276-10478557	K562	blood:	n/a	chr11:10477539-10477548 chr11:10477085-10477101 chr11:10478151-10478168
13	NFIC	chr11:10476218-10478049	GM12878	blood:	n/a	n/a
14	POLR2A	chr11:10476208-10478464	GM12892	blood:	n/a	n/a
15	POLR2A	chr11:10476431-10478456	GM12892	blood:	n/a	n/a
16	POLR2A	chr11:10475934-10478530	K562	blood:	n/a	n/a
17	POLR2A	chr11:10476246-10478376	K562	blood:	n/a	n/a
18	REST	chr11:10476904-10477786	K562	blood:	n/a	n/a
19	POLR2A	chr11:10476159-10477179	U87	brain:	n/a	n/a
20	MAZ	chr11:10476419-10477815	K562	blood:	n/a	chr11:10476971-10476981 chr11:10476970-10476979
21	RELA	chr11:10476445-10478359	GM15510	blood:	n/a	n/a
22	POLR2A	chr11:10476140-10477855	K562	blood:	n/a	n/a
23	ZMIZ1	chr11:10476339-10478347	K562	blood:	n/a	n/a
24	POLR2A	chr11:10476124-10477179	U87	brain:	n/a	n/a
25	MAX	chr11:10476367-10477139	K562	blood:	n/a	chr11:10476971-10476981 chr11:10476970-10476979
26	GATA1	chr11:10477087-10478523	PBDE	blood:	n/a	chr11:10477539-10477548 chr11:10478151-10478168
27	JUND	chr11:10476349-10478384	K562	blood:	n/a	chr11:10476625-10476633 chr11:10476624-10476634 chr11:10477854-10477864 chr11:10476624-10476634 chr11:10478179-10478190 chr11:10477748-10477762 chr11:10476623-10476634
28	ZBTB7A	chr11:10476824-10477160	K562	blood:	n/a	n/a
29	POLR2A	chr11:10476429-10478304	GM12891	blood:	n/a	n/a
30	POLR2A	chr11:10476252-10478232	GM12892	blood:	n/a	n/a
31	POLR2A	chr11:10477111-10478375	GM12878	blood:	n/a	n/a
32	POLR2A	chr11:10476083-10478011	K562	blood:	n/a	n/a
33	MYC	chr11:10476323-10478411	NB4	blood:	n/a	chr11:10476971-10476981 chr11:10476970-10476979
34	HEY1	chr11:10477109-10477885	K562	blood:	n/a	n/a
35	POLR2A	chr11:10476101-10477850	K562	blood:	n/a	n/a
36	POLR2A	chr11:10476324-10478186	GM12892	blood:	n/a	n/a
37	MAX	chr11:10476210-10478179	HCT-116	colon:	n/a	chr11:10476971-10476981 chr11:10476970-10476979
38	MXI1	chr11:10476098-10479047	IMR90	lung:	n/a	chr11:10476482-10476491 chr11:10476971-10476980
39	MAX	chr11:10476308-10478460	K562	blood:	n/a	chr11:10476971-10476981 chr11:10476970-10476979
40	EP300	chr11:10476307-10478383	K562	blood:	n/a	n/a
41	KAP1	chr11:10476246-10478054	HEK293	kidney:	n/a	n/a
42	POLR2A	chr11:10475962-10478174	U87	brain:	n/a	n/a
43	RCOR1	chr11:10476383-10478413	K562	blood:	n/a	n/a
44	STAT5A	chr11:10476952-10478243	GM12878	blood:	n/a	chr11:10477128-10477136
45	PML	chr11:10476262-10477189	GM12878	blood:	n/a	n/a
46	POLR2A	chr11:10476091-10477170	HCT-116	colon:	n/a	n/a
47	MAX	chr11:10476188-10478477	HCT-116	colon:	n/a	chr11:10476971-10476981 chr11:10476970-10476979
48	CBX3	chr11:10476267-10478447	K562	blood:	n/a	n/a
49	SIN3AK20	chr11:10476243-10478281	HCT-116	colon:	n/a	n/a
50	PML	chr11:10477045-10477876	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:10427808..10432250-chr11:10475440..10478017,5	K562	blood:
2	chr11:10470733..10474944-chr11:10476648..10480616,5	MCF-7	breast:
3	chr11:10469398..10472547-chr11:10473380..10477623,4	K562	blood:
4	chr11:10476262..10479144-chr11:10482528..10484355,2	K562	blood:
5	chr11:10476884..10479039-chr11:10561132..10563728,3	K562	blood:

Variant related genes	Relation type
AMPD3	TF binding region
ENSG00000133805	Chromatin interaction
ENSG00000177112	Chromatin interaction
ENSG00000110315	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10840419	0.94[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10840420	0.81[ASN][1000 genomes]
rs10840422	0.81[ASN][1000 genomes]
rs11042811	0.98[ASN][1000 genomes]
rs11042812	0.98[ASN][1000 genomes]
rs11602632	0.86[ASN][1000 genomes]
rs11604780	0.84[ASN][1000 genomes]
rs11604833	1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs11604838	0.87[ASN][1000 genomes]
rs11606703	0.87[ASN][1000 genomes]
rs2071020	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4909932	0.80[JPT][hapmap]
rs4910141	0.80[JPT][hapmap]
rs6484290	1.00[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs7111970	0.87[ASN][1000 genomes]
rs7112321	0.89[ASN][1000 genomes]
rs7119498	0.90[JPT][hapmap]
rs7929999	0.88[ASN][1000 genomes]
rs7938316	0.93[ASN][1000 genomes]
rs936513	0.95[ASN][1000 genomes]
rs9971562	0.94[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]

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	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv896990	chr11:10458596-10514707	Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs899010	OR10A6	cis	parietal	SCAN
rs899010	AMPD3	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10473000-10478400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:10473200-10477200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:10473200-10477200	Weak transcription	Liver	Liver
4	chr11:10473200-10478000	Enhancers	HMEC	breast
5	chr11:10473200-10512000	Weak transcription	Aorta	Aorta
6	chr11:10473600-10477200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr11:10473600-10477200	Weak transcription	Right Atrium	heart
8	chr11:10473600-10477400	Weak transcription	Right Ventricle	heart
9	chr11:10473600-10477800	Weak transcription	Lung	lung
10	chr11:10473600-10477800	Weak transcription	Pancreas	Pancrea
11	chr11:10474200-10482800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:10474400-10477600	Enhancers	Brain Substantia Nigra	brain
13	chr11:10475400-10477200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr11:10475400-10477600	Enhancers	Fetal Muscle Leg	muscle
15	chr11:10475600-10477200	Enhancers	Primary B cells from peripheral blood	blood
16	chr11:10475600-10477200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr11:10475600-10477200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr11:10475600-10477200	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr11:10475600-10477200	Enhancers	Brain Cingulate Gyrus	brain
20	chr11:10475600-10477200	Enhancers	Fetal Thymus	thymus
21	chr11:10475600-10478600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr11:10475800-10477200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr11:10475800-10477200	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr11:10476000-10477200	Enhancers	Primary T cells from cord blood	blood
25	chr11:10476000-10477200	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr11:10476000-10477200	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr11:10476000-10477400	Enhancers	Thymus	Thymus
28	chr11:10476000-10477600	Enhancers	Fetal Intestine Small	intestine
29	chr11:10476000-10477600	Bivalent Enhancer	Fetal Stomach	stomach
30	chr11:10476200-10477200	Flanking Active TSS	Hela-S3	cervix
31	chr11:10476200-10477800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:10476200-10478000	Flanking Active TSS	NHEK	skin
33	chr11:10476200-10478400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr11:10476200-10478400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr11:10476200-10478400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr11:10476200-10478800	Flanking Active TSS	Brain Hippocampus Middle	brain
37	chr11:10476400-10477200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr11:10476400-10477200	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr11:10476400-10477200	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr11:10476400-10477200	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr11:10476400-10477200	Enhancers	Primary T cells fromperipheralblood	blood
42	chr11:10476400-10477200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr11:10476400-10477200	Bivalent Enhancer	HepG2	liver
44	chr11:10476400-10477400	Enhancers	Stomach Mucosa	stomach
45	chr11:10476400-10478400	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr11:10476400-10478600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr11:10476400-10478600	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr11:10476400-10479000	Flanking Active TSS	GM12878-XiMat	blood
49	chr11:10476400-10481400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr11:10476600-10477200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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