Variant report

Variant	rs4929912
Chromosome Location	chr11:8816695-8816696
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	CTCF	chr11:8816330-8816699	H1-hESC	embryonic stem cell:	n/a	chr11:8816539-8816552 chr11:8816540-8816549
2	SMC3	chr11:8816305-8816764	HepG2	liver:	n/a	n/a
3	MAZ	chr11:8816194-8816986	HepG2	liver:	n/a	chr11:8816590-8816600
4	RAD21	chr11:8816181-8816901	HCT-116	colon:	n/a	chr11:8816536-8816550
5	FOXA1	chr11:8816234-8816728	HepG2	liver:	n/a	n/a
6	RAD21	chr11:8816195-8816764	H1-hESC	embryonic stem cell:	n/a	chr11:8816536-8816550
7	RAD21	chr11:8816276-8816739	MCF-7	breast:	n/a	chr11:8816536-8816550
8	RAD21	chr11:8816333-8816750	HepG2	liver:	n/a	chr11:8816536-8816550
9	RAD21	chr11:8816256-8816721	HepG2	liver:	n/a	chr11:8816536-8816550
10	SP1	chr11:8816123-8816701	HepG2	liver:	n/a	n/a
11	ARID3A	chr11:8816236-8816720	HepG2	liver:	n/a	n/a
12	MYBL2	chr11:8816180-8816755	HepG2	liver:	n/a	n/a
13	RAD21	chr11:8816162-8816789	HCT-116	colon:	n/a	chr11:8816536-8816550
14	FOXA2	chr11:8816209-8816855	A549	lung:	n/a	n/a
15	CTCF	chr11:8816520-8816910	HRE	kidney:	n/a	chr11:8816539-8816552 chr11:8816540-8816549
16	RAD21	chr11:8816355-8816705	H1-hESC	embryonic stem cell:	n/a	chr11:8816536-8816550
17	STAT3	chr11:8816576-8816697	MCF10A-Er-Src	breast:	n/a	chr11:8816605-8816616
18	FOXA1	chr11:8816247-8816805	HepG2	liver:	n/a	n/a
19	CTCF	chr11:8816314-8816762	HepG2	liver:	n/a	chr11:8816539-8816552 chr11:8816540-8816549
20	ZEB1	chr11:8815688-8816921	HepG2	liver:	n/a	chr11:8816556-8816564 chr11:8816229-8816236
21	MAFF	chr11:8816150-8816698	HepG2	liver:	n/a	chr11:8816315-8816329
22	ZEB1	chr11:8815847-8816793	HepG2	liver:	n/a	chr11:8816556-8816564 chr11:8816229-8816236
23	NFIC	chr11:8816152-8816716	HepG2	liver:	n/a	n/a
24	MBD4	chr11:8816120-8816723	HepG2	liver:	n/a	n/a
25	RAD21	chr11:8816216-8816724	HepG2	liver:	n/a	chr11:8816536-8816550
26	MXI1	chr11:8815823-8816702	HepG2	liver:	n/a	chr11:8815935-8815944 chr11:8815933-8815942
27	CTCF	chr11:8816600-8816750	A549	lung:	n/a	n/a
28	CTCF	chr11:8816376-8816704	K562	blood:	n/a	chr11:8816539-8816552 chr11:8816540-8816549
29	EP300	chr11:8816207-8816730	HepG2	liver:	n/a	n/a
30	FOXA1	chr11:8816180-8816771	HepG2	liver:	n/a	n/a
31	CTCF	chr11:8816375-8816739	A549	lung:	n/a	chr11:8816539-8816552 chr11:8816540-8816549
32	CTCF	chr11:8816205-8816844	HCT-116	colon:	n/a	chr11:8816539-8816552 chr11:8816540-8816549
33	TEAD4	chr11:8816203-8816826	HepG2	liver:	n/a	n/a
34	MYC	chr11:8816577-8816756	H1-hESC	embryonic stem cell:	n/a	chr11:8816590-8816600
35	RAD21	chr11:8816396-8816725	A549	lung:	n/a	chr11:8816536-8816550
36	FOXA1	chr11:8816265-8816750	HepG2	liver:	n/a	n/a
37	FOXA2	chr11:8816381-8816782	A549	lung:	n/a	n/a
38	CTCF	chr11:8816398-8816697	GM12878	blood:	n/a	chr11:8816539-8816552 chr11:8816540-8816549

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8708277..8712745-chr11:8814108..8817920,5	MCF-7	breast:

Variant related genes	Relation type
ST5	TF binding region
ENSG00000166441	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10743093	0.81[CEU][hapmap]
rs10769947	1.00[CEU][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10769948	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10769955	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10769957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10769958	0.96[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10769967	0.81[CEU][hapmap]
rs10769970	0.81[CEU][hapmap]
rs10769973	0.81[CEU][hapmap]
rs10840130	0.81[AMR][1000 genomes]
rs10840134	0.84[CEU][hapmap]
rs10840141	0.81[CEU][hapmap]
rs10840142	0.81[CEU][hapmap]
rs10840148	0.81[CEU][hapmap]
rs11042055	0.96[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11042059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11042060	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11042067	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11042069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042078	0.80[AMR][1000 genomes]
rs11042079	0.80[AMR][1000 genomes]
rs11042103	0.81[CEU][hapmap]
rs12224436	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421789	0.96[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1529641	0.82[CEU][hapmap]
rs2316865	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568043	0.81[CEU][hapmap]
rs2568061	0.81[CEU][hapmap]
rs2568065	0.81[CEU][hapmap]
rs2568090	0.81[CEU][hapmap]
rs3763918	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3794153	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4579928	0.96[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4929911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4929914	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4929916	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61876187	0.80[AMR][1000 genomes]
rs6484484	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6484496	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7107867	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7123429	0.81[CEU][hapmap]
rs7129667	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7937298	0.81[CEU][hapmap]
rs7944560	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945705	0.81[CEU][hapmap]
rs905290	0.96[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][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	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv553447	chr11:8792622-8825966	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv527920	chr11:8816695-8856822	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4929912	OR52A1	cis	parietal	SCAN
rs4929912	OR52E8	cis	cerebellum	SCAN
rs4929912	TMEM9B-AS1	cis	lung	GTEx
rs4929912	RRP8	cis	parietal	SCAN
rs4929912	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs4929912	TRIM66	cis	lung	GTEx
rs4929912	C11orf17	cis	multi-tissue	Pritchard
rs4929912	OR51B6	cis	parietal	SCAN
rs4929912	C11orf17	cis	cerebellum	SCAN
rs4929912	AKIP1	cis	Thyroid	GTEx
rs4929912	APBB1	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8797800-8827200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:8800800-8822400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr11:8800800-8825800	Weak transcription	Brain Angular Gyrus	brain
4	chr11:8800800-8827400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:8801600-8820000	Weak transcription	HSMMtube	muscle
6	chr11:8801600-8827400	Weak transcription	Esophagus	oesophagus
7	chr11:8802200-8819200	Weak transcription	NH-A	brain
8	chr11:8803000-8820600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr11:8808600-8819400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr11:8809000-8830200	Weak transcription	Fetal Brain Male	brain
11	chr11:8809200-8826600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr11:8809200-8829200	Weak transcription	Fetal Kidney	kidney
13	chr11:8810600-8820600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr11:8811800-8827000	Weak transcription	HMEC	breast
15	chr11:8811800-8828600	Weak transcription	Hela-S3	cervix
16	chr11:8811800-8828800	Weak transcription	Aorta	Aorta
17	chr11:8811800-8830400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr11:8811800-8830600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:8812400-8820600	Weak transcription	Right Ventricle	heart
20	chr11:8813800-8817600	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr11:8814200-8817000	Enhancers	Rectal Smooth Muscle	rectum
22	chr11:8814200-8817200	Enhancers	Colon Smooth Muscle	Colon
23	chr11:8814200-8828400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr11:8814600-8817400	Weak transcription	NHEK	skin
25	chr11:8814800-8825400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr11:8815000-8827800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:8815200-8817000	Enhancers	Fetal Intestine Large	intestine
28	chr11:8815200-8818200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr11:8815200-8818800	Weak transcription	Adipose Nuclei	Adipose
30	chr11:8815200-8826800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr11:8815400-8817000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
32	chr11:8815400-8818000	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr11:8815400-8818600	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr11:8815400-8819200	Weak transcription	Fetal Lung	lung
35	chr11:8815400-8820600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr11:8815400-8822000	Weak transcription	HUVEC	blood vessel
37	chr11:8815600-8817200	Genic enhancers	Fetal Muscle Leg	muscle
38	chr11:8815600-8822600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr11:8815600-8825200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr11:8815800-8816800	Enhancers	Psoas Muscle	Psoas
41	chr11:8815800-8816800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr11:8815800-8817000	Enhancers	Right Atrium	heart
43	chr11:8815800-8817200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr11:8815800-8817800	Strong transcription	Placenta	Placenta
45	chr11:8815800-8818200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr11:8815800-8827800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:8816000-8816800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr11:8816000-8816800	Enhancers	Colonic Mucosa	Colon
49	chr11:8816000-8817000	Enhancers	Fetal Heart	heart
50	chr11:8816000-8817800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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