Variant report

Variant	rs11235707
Chromosome Location	chr11:72982993-72982994
allele	C/T
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	ATF3	chr11:72982904-72983567	A549	lung:	n/a	n/a
2	IKZF1	chr11:72982782-72983458	GM12878	blood:	n/a	n/a
3	TFAP2C	chr11:72982938-72983389	Hela-S3	cervix:	n/a	chr11:72983156-72983171
4	GATA3	chr11:72982439-72983324	SH-SY5Y	brain:	n/a	chr11:72982906-72982915 chr11:72982897-72982914
5	SP1	chr11:72982747-72983901	A549	lung:	n/a	chr11:72983727-72983741 chr11:72983730-72983742 chr11:72983732-72983741 chr11:72983647-72983661 chr11:72983732-72983741 chr11:72983731-72983740
6	USF1	chr11:72982952-72983495	A549	lung:	n/a	n/a
7	GATA3	chr11:72982903-72983581	MCF-7	breast:	n/a	chr11:72982906-72982915
8	FOSL2	chr11:72982763-72983976	A549	lung:	n/a	chr11:72983240-72983251
9	SP1	chr11:72982811-72983889	A549	lung:	n/a	chr11:72983727-72983741 chr11:72983730-72983742 chr11:72983732-72983741 chr11:72983647-72983661 chr11:72983732-72983741 chr11:72983731-72983740
10	TAF1	chr11:72982956-72983873	A549	lung:	n/a	n/a
11	FOXA1	chr11:72982954-72983396	HepG2	liver:	n/a	n/a
12	GATA3	chr11:72982717-72984003	A549	lung:	n/a	chr11:72982906-72982915 chr11:72982897-72982914
13	GATA3	chr11:72982849-72983529	MCF-7	breast:	n/a	chr11:72982906-72982915 chr11:72982897-72982914
14	FOXA2	chr11:72982963-72983482	A549	lung:	n/a	n/a
15	EP300	chr11:72982807-72983378	SK-N-SH_RA	brain:	n/a	n/a
16	TCF12	chr11:72982736-72984097	A549	lung:	n/a	n/a
17	GATA3	chr11:72982795-72983458	T-47D	breast:	n/a	chr11:72982906-72982915 chr11:72982897-72982914
18	SIN3AK20	chr11:72982727-72983644	MCF-7	breast:	n/a	n/a
19	MAX	chr11:72982810-72983965	A549	lung:	n/a	chr11:72983729-72983739
20	EP300	chr11:72982796-72983405	SK-N-SH_RA	brain:	n/a	n/a
21	BCL3	chr11:72982915-72983823	A549	lung:	n/a	n/a
22	MXI1	chr11:72982078-72985057	SK-N-SH	brain:	n/a	n/a
23	FOXA2	chr11:72982992-72983347	HepG2	liver:	n/a	n/a
24	EP300	chr11:72982825-72983491	A549	lung:	n/a	n/a
25	CTCF	chr11:72982940-72983090	AG04449	skin:	n/a	chr11:72983042-72983055
26	CREB1	chr11:72982961-72983843	A549	lung:	n/a	n/a
27	EP300	chr11:72979726-72985647	SK-N-SH	brain:	n/a	chr11:72985619-72985633 chr11:72984138-72984152 chr11:72981442-72981455 chr11:72984140-72984154 chr11:72984139-72984153 chr11:72981929-72981945
28	EP300	chr11:72982839-72983425	T-47D	breast:	n/a	n/a
29	HDAC2	chr11:72982835-72983568	MCF-7	breast:	n/a	n/a
30	POLR2A	chr11:72982848-72983087	SK-N-SH	brain:	n/a	n/a
31	GATA2	chr11:72982000-72983436	SH-SY5Y	brain:	n/a	chr11:72982906-72982915 chr11:72982897-72982914
32	FOXA1	chr11:72982921-72983457	T-47D	breast:	n/a	n/a
33	FOSL2	chr11:72982975-72983422	HepG2	liver:	n/a	chr11:72983240-72983251
34	MAX	chr11:72982718-72984853	A549	lung:	n/a	chr11:72983729-72983739 chr11:72984297-72984307
35	REST	chr11:72982868-72983403	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr11:72982818-72983385	SK-N-SH	brain:	n/a	n/a
37	FOXA2	chr11:72982786-72983454	HepG2	liver:	n/a	n/a
38	GABPA	chr11:72982960-72983544	A549	lung:	n/a	n/a
39	FOXA1	chr11:72982915-72983409	T-47D	breast:	n/a	n/a
40	EP300	chr11:72982963-72983408	HepG2	liver:	n/a	n/a
41	EP300	chr11:72982879-72983467	T-47D	breast:	n/a	n/a
42	GATA3	chr11:72982817-72983494	T-47D	breast:	n/a	chr11:72982906-72982915 chr11:72982897-72982914
43	JUND	chr11:72982827-72983542	MCF-7	breast:	n/a	chr11:72983241-72983252
44	EP300	chr11:72982803-72983754	A549	lung:	n/a	n/a
45	FOXA1	chr11:72982958-72983387	HepG2	liver:	n/a	n/a
46	CTCF	chr11:72982920-72983070	SK-N-SH_RA	brain:	n/a	chr11:72983042-72983055
47	SPI1	chr11:72982432-72983082	GM12878	blood:	n/a	chr11:72983044-72983057
48	GATA3	chr11:72982751-72983403	SK-N-SH	brain:	n/a	chr11:72982906-72982915 chr11:72982897-72982914
49	YY1	chr11:72982789-72983334	SK-N-SH_RA	brain:	n/a	n/a
50	JUND	chr11:72982857-72983554	T-47D	breast:	n/a	chr11:72983241-72983252

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:72982950-72983000	NT2-D1	testis:	n/a
2	chr11:72982950-72983000	MCF10A-Er-Src	breast:	n/a
3	chr11:72982950-72983000	NH-A	brain:	n/a
4	chr11:72982950-72983000	ovcar-3	ovarian:	n/a
5	chr11:72982950-72983000	GM12891	blood:	n/a
6	chr11:72982950-72983000	HRCEpiC	kidney:	n/a
7	chr11:72982950-72983000	AG09309	skin:	n/a
8	chr11:72982950-72983000	Hepatocyte	liver:	n/a
9	chr11:72982950-72983000	HNPCEpiC	eye:	n/a
10	chr11:72982950-72983000	HRPEpiC	eye:	n/a
11	chr11:72982950-72983000	RPTEC	kidney:	n/a
12	chr11:72982950-72983000	HIPEpiC	eye:	n/a
13	chr11:72982950-72983000	HEEpiC	esophagus:	n/a
14	chr11:72982950-72983000	CMK	blood:	n/a
15	chr11:72982950-72983000	PANC-1	pancreas:	n/a
16	chr11:72982950-72983000	HCM	heart:	n/a
17	chr11:72982950-72983000	NB4	blood:	n/a
18	chr11:72982950-72983000	Jurkat	blood:	n/a
19	chr11:72982950-72983000	U87	brain:	n/a
20	chr11:72982950-72983000	LNCaP	prostate:	n/a
21	chr11:72982950-72983000	HCT-116	colon:	n/a
22	chr11:72982950-72983000	BJ	skin:	n/a
23	chr11:72982950-72983000	AoSMC	blood vessel:	n/a
24	chr11:72982950-72983000	Hela-S3	cervix:	n/a
25	chr11:72982950-72983000	Caco-2	colon:	n/a
26	chr11:72982950-72983000	K562	blood:	n/a
27	chr11:72982950-72983000	HCF	heart:	n/a
28	chr11:72982950-72983000	HMEC	breast:	n/a
29	chr11:72982950-72983000	GM12892	blood:	n/a
30	chr11:72982950-72983000	HAEpiC	amniotic membrane:	n/a
31	chr11:72982950-72983000	HCPEpiC	choroid plexus:	n/a
32	chr11:72982950-72983000	HepG2	liver:	n/a
33	chr11:72982950-72983000	IMR90	lung:	fetal
34	chr11:72982950-72983000	SK-N-SH_RA	brain:	n/a
35	chr11:72982950-72983000	ProgFib	skin:	n/a
36	chr11:72982950-72983000	HEK293	kidney:	embryo
37	chr11:72982950-72983000	ECC-1	luminal epithelium:	n/a
38	chr11:72982950-72983000	GM06990	blood:	n/a
39	chr11:72982950-72983000	A549	lung:	n/a
40	chr11:72982950-72983000	GM12878	blood:	n/a
41	chr11:72982950-72983000	SK-N-SH	brain:	n/a
42	chr11:72982950-72983000	HPAEpiC	pulmonary alveolar:	n/a
43	chr11:72982950-72983000	AG04449	skin:	fetal
44	chr11:72982950-72983000	AG04450	lung:	fetal
45	chr11:72982950-72983000	AG10803	skin:	n/a
46	chr11:72982950-72983000	SKMC	muscle:	n/a
47	chr11:72982950-72983000	NHBE	bronchial:	n/a
48	chr11:72982950-72983000	MCF-7	breast:	n/a
49	chr11:72982950-72983000	PFSK-1	brain:	n/a
50	chr11:72982950-72983000	NHDF-neo	bronchial:	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:72980434..72984433-chr11:73015744..73020345,4	MCF-7	breast:
2	chr11:72974009..72977358-chr11:72978806..72983362,4	MCF-7	breast:
3	chr11:72979299..72983458-chr11:73018365..73020880,3	MCF-7	breast:

Variant related genes	Relation type
P2RY6	TF binding region
P2RY6	CpG island
ENSG00000257038	Chromatin interaction
ENSG00000110237	Chromatin interaction
ENSG00000171631	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10898913	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10898914	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10898915	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235699	1.00[JPT][hapmap]
rs11235701	0.95[ASN][1000 genomes]
rs11235703	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235705	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235706	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MKK][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235708	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235709	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235712	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235713	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12276627	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12363628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12787775	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12790447	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12790863	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12794405	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12801084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12808111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1894075	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28513476	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34023835	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34385073	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35455220	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35963948	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4432047	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6592517	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67897720	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7103650	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7106903	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7114877	0.95[ASN][1000 genomes]
rs7116594	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7123808	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7127013	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7127179	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7127705	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7127940	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7925649	1.00[JPT][hapmap]
rs7930891	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7942649	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882904	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9988805	1.00[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	nsv832208	chr11:72876184-73091003	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv1821041	chr11:72937162-73113080	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11235707	PAAF1	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72976400-72984800	Enhancers	Placenta Amnion	Placenta Amnion
2	chr11:72977000-72983200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:72977200-72991600	Weak transcription	Osteobl	bone
4	chr11:72978000-72986000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr11:72979000-72984200	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr11:72979800-72984000	Enhancers	Spleen	Spleen
7	chr11:72980000-72983600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr11:72980400-72983400	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr11:72980400-72983600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:72980400-72987200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr11:72980400-72998400	Weak transcription	Right Atrium	heart
12	chr11:72980600-72983000	Enhancers	Duodenum Mucosa	Duodenum
13	chr11:72980600-72984000	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr11:72981200-72985600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr11:72981200-72985600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr11:72981200-72991000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr11:72981400-72983000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr11:72981400-72983000	Weak transcription	Esophagus	oesophagus
19	chr11:72981400-72983400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr11:72981600-72983000	Weak transcription	Left Ventricle	heart
21	chr11:72981600-72983200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr11:72981600-72984000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr11:72981600-72984400	Weak transcription	Lung	lung
24	chr11:72981800-72983000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr11:72981800-72983200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr11:72981800-72983400	Weak transcription	Fetal Muscle Leg	muscle
27	chr11:72981800-72984000	Enhancers	Fetal Heart	heart
28	chr11:72982000-72984400	Weak transcription	Fetal Lung	lung
29	chr11:72982000-72984800	Weak transcription	Small Intestine	intestine
30	chr11:72982200-72983000	Enhancers	Primary B cells from peripheral blood	blood
31	chr11:72982200-72983000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr11:72982200-72983000	Flanking Active TSS	GM12878-XiMat	blood
33	chr11:72982200-72983400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
34	chr11:72982200-72983400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr11:72982400-72983400	Flanking Active TSS	HepG2	liver
36	chr11:72982600-72983000	Enhancers	Placenta	Placenta
37	chr11:72982600-72983200	Enhancers	Fetal Intestine Small	intestine
38	chr11:72982600-72986000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr11:72982800-72983000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr11:72982800-72983000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr11:72982800-72983400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr11:72982800-72983400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr11:72982800-72983400	Enhancers	Fetal Intestine Large	intestine
44	chr11:72982800-72983600	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr11:72982800-72983600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:72982800-72983600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr11:72982800-72983600	Bivalent Enhancer	K562	blood
48	chr11:72982800-72983600	Enhancers	NHEK	skin
49	chr11:72982800-72983800	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr11:72982800-72983800	Enhancers	Hela-S3	cervix

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