Variant report

Variant	rs2729353
Chromosome Location	chr11:57248003-57248004
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	CTCF	chr11:57247920-57248070	MCF-7	breast:	n/a	chr11:57247964-57247982
2	CTCF	chr11:57247920-57248070	GM12865	blood:	n/a	chr11:57247964-57247982
3	ZC3H11A	chr11:57247866-57248109	K562	blood:	n/a	n/a
4	MYC	chr11:57247907-57248028	MCF10A-Er-Src	breast:	n/a	n/a
5	NANOG	chr11:57247811-57248078	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr11:57247940-57248090	SAEC	small airway:	n/a	chr11:57247964-57247982
7	POLR2A	chr11:57246787-57248518	HepG2	liver:	n/a	n/a
8	RAD21	chr11:57247841-57248166	H1-hESC	embryonic stem cell:	n/a	chr11:57247962-57247981
9	RAD21	chr11:57247800-57248088	GM12878	blood:	n/a	chr11:57247962-57247981
10	CTCF	chr11:57247900-57248050	GM12872	blood:	n/a	chr11:57247964-57247982
11	CTCF	chr11:57247840-57248107	GM10248	blood:	n/a	chr11:57247964-57247982
12	CTCF	chr11:57247900-57248050	HMEC	breast:	n/a	chr11:57247964-57247982
13	CTCF	chr11:57247880-57248030	AG09309	skin:	n/a	chr11:57247964-57247982
14	CTCF	chr11:57247844-57248118	GM10266	blood:	n/a	chr11:57247964-57247982
15	CTCF	chr11:57247860-57248010	HepG2	liver:	n/a	chr11:57247964-57247982
16	MAZ	chr11:57247800-57248156	K562	blood:	n/a	n/a
17	CTCF	chr11:57247781-57248154	T-47D	breast:	n/a	chr11:57247964-57247982
18	CBX3	chr11:57247679-57248211	K562	blood:	n/a	n/a
19	CTCF	chr11:57247900-57248050	GM12867	blood:	n/a	chr11:57247964-57247982
20	CTCF	chr11:57247900-57248050	K562	blood:	n/a	chr11:57247964-57247982
21	CTCF	chr11:57247900-57248050	Hela-S3	cervix:	n/a	chr11:57247964-57247982
22	CTCF	chr11:57247718-57248192	A549	lung:	n/a	chr11:57247964-57247982
23	RAD21	chr11:57247811-57248157	HepG2	liver:	n/a	chr11:57247962-57247981
24	CTCF	chr11:57247860-57248010	GM12873	blood:	n/a	chr11:57247964-57247982
25	SMC3	chr11:57247820-57248873	HepG2	liver:	n/a	chr11:57248283-57248293 chr11:57247966-57247980
26	CTCF	chr11:57247860-57248010	HPAF	blood vessel:	n/a	chr11:57247964-57247982
27	CTCF	chr11:57247900-57248050	GM12868	blood:	n/a	chr11:57247964-57247982
28	CTCF	chr11:57247860-57248010	SAEC	small airway:	n/a	chr11:57247964-57247982
29	CTCF	chr11:57247960-57248110	NHDF-neo	bronchial:	n/a	chr11:57247964-57247982
30	CTCF	chr11:57247920-57248070	K562	blood:	n/a	chr11:57247964-57247982
31	RAD21	chr11:57247866-57248062	K562	blood:	n/a	chr11:57247962-57247981
32	FOXA1	chr11:57247827-57248061	T-47D	breast:	n/a	n/a
33	CTCF	chr11:57247855-57248098	MCF-7	breast:	n/a	chr11:57247964-57247982
34	RAD21	chr11:57247842-57248120	SK-N-SH_RA	brain:	n/a	chr11:57247962-57247981
35	ARID3A	chr11:57247879-57248515	HepG2	liver:	n/a	n/a
36	ARID3A	chr11:57247942-57248228	K562	blood:	n/a	n/a
37	CTCF	chr11:57247940-57248090	HAc	cerebellar:	n/a	chr11:57247964-57247982
38	CTCF	chr11:57247900-57248050	GM12870	blood:	n/a	chr11:57247964-57247982
39	CTCF	chr11:57247854-57248104	LNCaP	prostate:	n/a	chr11:57247964-57247982
40	CTCF	chr11:57247900-57248050	HBMEC	blood vessel:	n/a	chr11:57247964-57247982
41	CTCF	chr11:57247708-57248311	HCT-116	colon:	n/a	chr11:57248282-57248292 chr11:57247964-57247982
42	CTCF	chr11:57247900-57248050	AG10803	skin:	n/a	chr11:57247964-57247982
43	CTCF	chr11:57247880-57248030	HA-sp	spinal cord:	n/a	chr11:57247964-57247982
44	ZNF143	chr11:57247801-57248151	GM12878	blood:	n/a	n/a
45	CTCF	chr11:57247752-57248175	GM12878	blood:	n/a	chr11:57247964-57247982
46	CTCF	chr11:57247814-57248129	GM12892	blood:	n/a	chr11:57247964-57247982
47	CTCF	chr11:57247879-57248088	GM13976	blood:	n/a	chr11:57247964-57247982
48	CTCF	chr11:57247920-57248070	GM12871	blood:	n/a	chr11:57247964-57247982
49	CTCF	chr11:57247900-57248050	HEEpiC	esophagus:	n/a	chr11:57247964-57247982
50	KAP1	chr11:57247715-57248090	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:57225632..57226815-chr11:57247626..57248661,4	K562	blood:
2	chr11:57227036..57227650-chr11:57247534..57248049,2	K562	blood:
3	chr11:57247726..57251510-chr11:57253790..57259247,6	K562	blood:
4	chr11:57245031..57247127-chr11:57247406..57249542,2	K562	blood:
5	chr11:57241323..57242908-chr11:57245144..57248142,2	MCF-7	breast:
6	chr11:57243845..57245623-chr11:57246528..57248999,2	MCF-7	breast:
7	chr11:57246699..57250241-chr11:57294566..57299733,5	K562	blood:
8	chr11:57241042..57244897-chr11:57245318..57249265,7	K562	blood:
9	chr11:57247589..57249492-chr11:57297953..57299555,2	MCF-7	breast:
10	chr11:57197604..57200405-chr11:57246413..57248386,2	K562	blood:
11	chr11:57189022..57190886-chr11:57246954..57249146,2	K562	blood:

Variant related genes	Relation type
ENSG00000255301	TF binding region
ENSG00000134809	Chromatin interaction
ENSG00000255301	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1001956	0.95[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2250673	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2258835	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2467327	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2509899	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2511984	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2511986	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2581921	0.84[ASN][1000 genomes]
rs2581922	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2581923	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2584856	1.00[CEU][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2584862	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2649667	0.95[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2729363	0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2729377	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2729384	1.00[CEU][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2729387	0.86[EUR][1000 genomes]
rs2729394	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2848626	0.82[ASN][1000 genomes]
rs2848634	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2848635	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2848640	1.00[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3851117	0.90[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs2729353	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs2729353	TIMM10	cis	lymphoblastoid	seeQTL
rs2729353	TIMM10	cis	Heart Left Ventricle	GTEx
rs2729353	TIMM10	cis	cerebellum	SCAN
rs2729353	OR10Q1	cis	parietal	SCAN
rs2729353	TIMM10	cis	Artery Tibial	GTEx
rs2729353	TIMM10	cis	multi-tissue	Pritchard
rs2729353	SLC43A1	cis	cerebellum	SCAN
rs2729353	TIMM10	cis	parietal	SCAN
rs2729353	OR5AP2	cis	parietal	SCAN
rs2729353	SLC43A1	cis	parietal	SCAN
rs2729353	SLC43A3	cis	cerebellum	SCAN
rs2729353	CMPK1	trans	parietal	SCAN
rs2729353	TIMM10	cis	Esophagus Muscularis	GTEx
rs2729353	TIMM10	cis	Artery Aorta	GTEx
rs2729353	TIMM10	cis	Esophagus Mucosa	GTEx
rs2729353	TIMM10	cis	Thyroid	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57244000-57250400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr11:57244400-57249600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr11:57244600-57250000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr11:57244600-57250000	Weak transcription	Ovary	ovary
5	chr11:57244600-57250000	Enhancers	A549	lung
6	chr11:57244600-57250400	Enhancers	Liver	Liver
7	chr11:57244600-57250400	Weak transcription	Right Atrium	heart
8	chr11:57244800-57249400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr11:57244800-57249400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr11:57244800-57249600	Weak transcription	Spleen	Spleen
11	chr11:57244800-57250000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr11:57245000-57248800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr11:57245000-57248800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr11:57245000-57249400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr11:57245000-57249400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr11:57245400-57249600	Weak transcription	Lung	lung
17	chr11:57245600-57250600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr11:57246400-57248200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:57247200-57249600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr11:57247200-57250400	Weak transcription	GM12878-XiMat	blood
21	chr11:57247200-57250600	Weak transcription	Gastric	stomach
22	chr11:57247200-57250600	Weak transcription	Pancreas	Pancrea
23	chr11:57247400-57249200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr11:57247600-57248400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
25	chr11:57247600-57248400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
26	chr11:57247600-57248600	Enhancers	K562	blood
27	chr11:57248000-57248400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr11:57248000-57248600	Flanking Active TSS	HepG2	liver

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