Variant report

Variant	rs2653565
Chromosome Location	chr11:8893193-8893194
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	YY1	chr11:8892805-8893213	SK-N-SH_RA	brain:	n/a	chr11:8892824-8892838
2	TAF1	chr11:8891936-8893195	SK-N-SH	brain:	n/a	n/a
3	YY1	chr11:8892818-8893241	SK-N-SH_RA	brain:	n/a	chr11:8892824-8892838
4	RAD21	chr11:8892842-8893244	SK-N-SH_RA	brain:	n/a	chr11:8892968-8892978
5	REST	chr11:8892817-8893242	PFSK-1	brain:	n/a	chr11:8892828-8892841
6	MAX	chr11:8891836-8893222	ECC-1	luminal epithelium:	n/a	chr11:8892798-8892808 chr11:8892363-8892372 chr11:8892821-8892831 chr11:8892960-8892971
7	PBX3	chr11:8892634-8893313	SK-N-SH	brain:	n/a	n/a
8	KAP1	chr11:8892897-8893370	HEK293	kidney:	n/a	n/a
9	TCF12	chr11:8892777-8893303	ECC-1	luminal epithelium:	n/a	chr11:8892834-8892844 chr11:8893237-8893244
10	TCF12	chr11:8891785-8893450	SK-N-SH	brain:	n/a	chr11:8892834-8892844 chr11:8893237-8893244
11	USF1	chr11:8892643-8893256	HCT-116	colon:	n/a	chr11:8892960-8892971 chr11:8892827-8892843
12	E2F6	chr11:8892814-8893225	A549	lung:	n/a	chr11:8892820-8892829 chr11:8892831-8892841
13	SIN3AK20	chr11:8891931-8893274	PANC-1	pancreas:	n/a	n/a
14	MAX	chr11:8891686-8893209	Hela-S3	cervix:	n/a	chr11:8892798-8892808 chr11:8892363-8892372 chr11:8892821-8892831 chr11:8892960-8892971
15	SIN3A	chr11:8891922-8893230	H1-hESC	embryonic stem cell:	n/a	chr11:8892119-8892128
16	POLR2A	chr11:8892771-8893243	SK-N-MC	brain:	n/a	n/a
17	TCF7L2	chr11:8893001-8893365	HEK293	kidney:	n/a	n/a
18	SIN3AK20	chr11:8891835-8893265	SK-N-SH	brain:	n/a	n/a
19	TCF7L2	chr11:8892874-8893257	PANC-1	pancreas:	n/a	n/a
20	RAD21	chr11:8892824-8893216	SK-N-SH_RA	brain:	n/a	chr11:8892968-8892978
21	HA-E2F1	chr11:8891738-8893272	MCF-7	breast:	n/a	chr11:8892820-8892829 chr11:8892527-8892537 chr11:8892831-8892841 chr11:8892597-8892606
22	MAX	chr11:8892429-8893296	SK-N-SH	brain:	n/a	chr11:8892798-8892808 chr11:8892821-8892831 chr11:8892960-8892971
23	SP1	chr11:8892589-8893325	A549	lung:	n/a	chr11:8892819-8892831 chr11:8892820-8892829 chr11:8892677-8892687 chr11:8892816-8892830
24	MAX	chr11:8892697-8893248	A549	lung:	n/a	chr11:8892798-8892808 chr11:8892821-8892831 chr11:8892960-8892971
25	GTF2F1	chr11:8893034-8893238	H1-hESC	embryonic stem cell:	n/a	n/a
26	USF1	chr11:8892719-8893213	A549	lung:	n/a	chr11:8892960-8892971 chr11:8892827-8892843
27	EP300	chr11:8892821-8893198	SK-N-SH_RA	brain:	n/a	chr11:8892824-8892833 chr11:8892824-8892840
28	TEAD4	chr11:8892417-8893269	ECC-1	luminal epithelium:	n/a	n/a
29	USF1	chr11:8892803-8893240	A549	lung:	n/a	chr11:8892960-8892971 chr11:8892827-8892843
30	TCF12	chr11:8892551-8893410	SK-N-SH	brain:	n/a	chr11:8892834-8892844 chr11:8893237-8893244
31	POLR2A	chr11:8892452-8893243	SK-N-MC	brain:	n/a	n/a
32	POLR2A	chr11:8891842-8893197	ProgFib	skin:	n/a	n/a
33	SMC3	chr11:8892869-8893205	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr11:8891796-8893325	SK-N-SH	brain:	n/a	n/a
35	SP1	chr11:8892771-8893226	A549	lung:	n/a	chr11:8892819-8892831 chr11:8892820-8892829 chr11:8892816-8892830
36	POLR2A	chr11:8891804-8893331	PFSK-1	brain:	n/a	n/a
37	PBX3	chr11:8892403-8893277	SK-N-SH	brain:	n/a	n/a
38	TBP	chr11:8891988-8893256	H1-hESC	embryonic stem cell:	n/a	n/a
39	TCF7L2	chr11:8892878-8893288	Hela-S3	cervix:	n/a	n/a
40	CTCF	chr11:8893180-8893330	NHDF-neo	bronchial:	n/a	n/a
41	EP300	chr11:8892766-8893198	SK-N-SH_RA	brain:	n/a	chr11:8892824-8892833 chr11:8892824-8892840
42	JUND	chr11:8892799-8893270	A549	lung:	n/a	chr11:8893033-8893047 chr11:8892819-8892828
43	YY1	chr11:8892816-8893260	SK-N-SH	brain:	n/a	chr11:8892824-8892838
44	TAF1	chr11:8891809-8893236	PFSK-1	brain:	n/a	n/a
45	USF1	chr11:8892654-8893273	SK-N-SH	brain:	n/a	chr11:8892960-8892971 chr11:8892827-8892843
46	TCF12	chr11:8892545-8893395	A549	lung:	n/a	chr11:8892834-8892844 chr11:8893237-8893244
47	EP300	chr11:8891727-8893408	SK-N-SH	brain:	n/a	chr11:8892357-8892366 chr11:8892824-8892833 chr11:8892594-8892603 chr11:8892824-8892840 chr11:8892521-8892537
48	TCF12	chr11:8892755-8893217	A549	lung:	n/a	chr11:8892834-8892844
49	POLR2A	chr11:8891823-8893243	PFSK-1	brain:	n/a	n/a
50	E2F6	chr11:8892687-8893363	A549	lung:	n/a	chr11:8892820-8892829 chr11:8892831-8892841

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8706918..8709095-chr11:8891415..8893255,2	MCF-7	breast:
2	chr11:8891163..8893518-chr11:8931818..8934397,2	MCF-7	breast:

Variant related genes	Relation type
ST5	TF binding region
ENSG00000212607	Chromatin interaction
ENSG00000166452	Chromatin interaction
ENSG00000166444	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10219366	0.89[EUR][1000 genomes]
rs1025438	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs10734639	0.91[CEU][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs10769974	0.91[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs10769976	0.90[EUR][1000 genomes]
rs10769977	0.91[CEU][hapmap]
rs10840150	0.82[EUR][1000 genomes]
rs10840151	0.91[CEU][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs10840154	0.91[CEU][hapmap]
rs10840156	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11042121	0.84[EUR][1000 genomes]
rs1136966	0.86[MEX][hapmap]
rs12794962	0.81[MEX][hapmap]
rs12798311	0.94[EUR][1000 genomes]
rs2016844	0.85[ASW][hapmap];1.00[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2056903	0.84[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2116510	0.91[CEU][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs2116511	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs2163625	0.91[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs2246878	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2247038	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2568029	0.90[MEX][hapmap]
rs2568034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2568042	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2568047	0.81[MEX][hapmap];0.81[TSI][hapmap]
rs2568069	0.91[CEU][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs2568074	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2568075	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2568077	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2568079	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes]
rs2568081	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs2568086	0.89[EUR][1000 genomes]
rs2653556	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2653560	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2653562	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2653587	0.84[EUR][1000 genomes]
rs2653601	0.85[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2653604	0.91[CEU][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs2653611	0.91[EUR][1000 genomes]
rs2742487	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs2742488	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs2742491	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs2742493	0.96[CEU][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs2742495	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes]
rs2742496	1.00[CEU][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs2742497	1.00[CEU][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs2742504	0.91[EUR][1000 genomes]
rs2742505	0.91[EUR][1000 genomes]
rs2742512	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2742513	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2742514	0.91[CEU][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs2742519	0.91[CEU][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs2742520	0.82[EUR][1000 genomes]
rs2742521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3751063	1.00[CEU][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs3751066	0.91[CEU][hapmap]
rs3751068	0.91[CEU][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs3763911	0.96[CEU][hapmap]
rs3763912	0.96[CEU][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs4909951	1.00[CEU][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs4910068	0.88[LWK][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap]
rs4910181	0.85[EUR][1000 genomes]
rs7106539	0.87[EUR][1000 genomes]
rs7125458	0.81[MEX][hapmap]
rs7936201	0.81[MEX][hapmap]
rs909464	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9300096	1.00[CEU][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs982273	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer 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	31 gene(s)	inside rSNPs	diseases
5	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	esv3402630	chr11:8887304-8893757	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	esv3325077	chr11:8887314-8893755	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2653565	C11orf17	Cis_1M	lymphoblastoid	RTeQTL
rs2653565	OR52E6	cis	parietal	SCAN
rs2653565	C11orf17	cis	multi-tissue	Pritchard

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8891000-8893200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr11:8891000-8893200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr11:8891200-8893600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr11:8891400-8893200	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr11:8891400-8893200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr11:8891400-8893200	Active TSS	Brain Anterior Caudate	brain
7	chr11:8891400-8893200	Active TSS	Colon Smooth Muscle	Colon
8	chr11:8891400-8893200	Active TSS	Duodenum Mucosa	Duodenum
9	chr11:8891400-8893200	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr11:8891400-8893400	Active TSS	Ovary	ovary
11	chr11:8891400-8894000	Active TSS	Stomach Smooth Muscle	stomach
12	chr11:8891600-8893200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:8891600-8893200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr11:8891600-8893200	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr11:8891600-8893200	Bivalent/Poised TSS	Fetal Thymus	thymus
16	chr11:8891600-8893200	Active TSS	Rectal Smooth Muscle	rectum
17	chr11:8891600-8893400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
18	chr11:8891600-8893400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:8891600-8893400	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr11:8891600-8893400	Active TSS	Right Atrium	heart
21	chr11:8891600-8893400	Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr11:8891600-8893600	Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr11:8891800-8893200	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr11:8891800-8893200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr11:8891800-8893200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr11:8891800-8893200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:8891800-8893200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr11:8891800-8893200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr11:8891800-8893200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:8891800-8893200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:8891800-8893200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr11:8891800-8893200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr11:8891800-8893200	Active TSS	Aorta	Aorta
34	chr11:8891800-8893200	Active TSS	Brain Angular Gyrus	brain
35	chr11:8891800-8893200	Active TSS	Colonic Mucosa	Colon
36	chr11:8891800-8893200	Active TSS	Esophagus	oesophagus
37	chr11:8891800-8893200	Active TSS	Fetal Brain Female	brain
38	chr11:8891800-8893200	Active TSS	Fetal Intestine Large	intestine
39	chr11:8891800-8893200	Active TSS	Fetal Kidney	kidney
40	chr11:8891800-8893200	Active TSS	Fetal Stomach	stomach
41	chr11:8891800-8893200	Active TSS	Left Ventricle	heart
42	chr11:8891800-8893200	Active TSS	Pancreas	Pancrea
43	chr11:8891800-8893200	Active TSS	Placenta Amnion	Placenta Amnion
44	chr11:8891800-8893200	Active TSS	Psoas Muscle	Psoas
45	chr11:8891800-8893200	Active TSS	Right Ventricle	heart
46	chr11:8891800-8893200	Active TSS	A549	lung
47	chr11:8891800-8893200	Active TSS	NHDF-Ad	bronchial
48	chr11:8891800-8893400	Active TSS	H1 Cell Line	embryonic stem cell
49	chr11:8891800-8893400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr11:8891800-8893400	Active TSS	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links