Variant report

Variant	rs35663729
Chromosome Location	chr12:50708870-50708871
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	RAD21	chr12:50708482-50708948	ECC-1	luminal epithelium:	n/a	n/a
2	CTCF	chr12:50708424-50709308	A549	lung:	n/a	chr12:50708654-50708675
3	CTCF	chr12:50708482-50709097	HCT-116	colon:	n/a	chr12:50708654-50708675
4	CHD1	chr12:50708420-50709302	IMR90	lung:	n/a	n/a
5	CTCF	chr12:50708820-50708970	GM12878	blood:	n/a	n/a
6	RAD21	chr12:50708434-50708954	MCF-7	breast:	n/a	n/a
7	CTCF	chr12:50708425-50708931	A549	lung:	n/a	chr12:50708654-50708675
8	MBD4	chr12:50708470-50708883	HepG2	liver:	n/a	n/a
9	RAD21	chr12:50708483-50708974	ECC-1	luminal epithelium:	n/a	n/a
10	CTCF	chr12:50708436-50708957	HCT-116	colon:	n/a	chr12:50708654-50708675
11	RAD21	chr12:50708468-50708872	GM12878	blood:	n/a	n/a
12	CTCF	chr12:50708511-50708948	H1-hESC	embryonic stem cell:	n/a	chr12:50708654-50708675
13	RAD21	chr12:50708263-50709092	HCT-116	colon:	n/a	n/a
14	CTCF	chr12:50708498-50708934	MCF-7	breast:	n/a	chr12:50708654-50708675
15	RAD21	chr12:50708450-50708904	HepG2	liver:	n/a	n/a
16	RAD21	chr12:50708263-50709115	SK-N-SH	brain:	n/a	n/a
17	CTCF	chr12:50708820-50708970	GM12864	blood:	n/a	n/a
18	SMC3	chr12:50708436-50708918	Hela-S3	cervix:	n/a	n/a
19	RFX5	chr12:50708416-50709299	SK-N-SH	brain:	n/a	chr12:50708852-50708860
20	CTCF	chr12:50708411-50709146	SK-N-SH	brain:	n/a	chr12:50708654-50708675
21	SMC3	chr12:50708420-50709270	SK-N-SH	brain:	n/a	n/a
22	RAD21	chr12:50708451-50709044	A549	lung:	n/a	n/a
23	RAD21	chr12:50708478-50709060	MCF-7	breast:	n/a	n/a
24	RAD21	chr12:50708417-50708938	H1-hESC	embryonic stem cell:	n/a	n/a
25	RAD21	chr12:50708435-50708904	SK-N-SH_RA	brain:	n/a	n/a
26	CTCF	chr12:50708478-50708916	MCF-7	breast:	n/a	chr12:50708654-50708675
27	RAD21	chr12:50708504-50708897	H1-hESC	embryonic stem cell:	n/a	n/a
28	RAD21	chr12:50708446-50708880	SK-N-SH_RA	brain:	n/a	n/a
29	RAD21	chr12:50708422-50709064	HCT-116	colon:	n/a	n/a
30	RAD21	chr12:50708447-50708887	IMR90	lung:	n/a	n/a
31	RAD21	chr12:50708429-50708954	HepG2	liver:	n/a	n/a
32	CTCF	chr12:50708860-50709010	HPF	lung:	n/a	n/a
33	RAD21	chr12:50708470-50708964	A549	lung:	n/a	n/a
34	CTCF	chr12:50708780-50708930	A549	lung:	n/a	n/a
35	CTCF	chr12:50708860-50709010	GM12871	blood:	n/a	n/a
36	CTCF	chr12:50708477-50708886	IMR90	lung:	n/a	chr12:50708654-50708675
37	SMC3	chr12:50708459-50708914	GM12878	blood:	n/a	n/a
38	RAD21	chr12:50708449-50708956	Hela-S3	cervix:	n/a	n/a
39	RAD21	chr12:50708446-50708870	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50575888..50577120-chr12:50707949..50709207,6	MCF-7	breast:
2	chr12:50575985..50576844-chr12:50708187..50709140,4	K562	blood:
3	chr12:50575251..50576960-chr12:50708135..50709374,12	MCF-7	breast:
4	chr12:50655178..50655736-chr12:50708248..50709081,3	MCF-7	breast:
5	chr12:50468671..50469657-chr12:50708194..50709149,5	K562	blood:

Variant related genes	Relation type
ENSG00000203425	TF binding region
ENSG00000203421	TF binding region
ENSG00000050405	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10783344	0.85[EUR][1000 genomes]
rs10783349	0.86[EUR][1000 genomes]
rs10783350	0.86[EUR][1000 genomes]
rs10876013	0.83[EUR][1000 genomes]
rs10876014	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10876015	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10876016	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10876017	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10876018	0.86[EUR][1000 genomes]
rs11169317	0.81[EUR][1000 genomes]
rs11169322	0.83[EUR][1000 genomes]
rs11169331	0.82[EUR][1000 genomes]
rs11169332	0.82[EUR][1000 genomes]
rs11169335	0.82[EUR][1000 genomes]
rs11169339	0.85[EUR][1000 genomes]
rs11169345	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11169347	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11169348	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11169349	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11169350	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11169351	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11169357	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11169359	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11169360	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11169367	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11169369	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11169370	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11169371	0.83[EUR][1000 genomes]
rs11169373	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11169374	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11169375	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11169376	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11169377	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11169379	0.86[EUR][1000 genomes]
rs11169386	0.85[EUR][1000 genomes]
rs11836169	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11838347	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12312177	0.80[AMR][1000 genomes]
rs12424691	0.83[EUR][1000 genomes]
rs12424713	0.83[EUR][1000 genomes]
rs12425229	0.83[EUR][1000 genomes]
rs12425705	0.82[EUR][1000 genomes]
rs12426444	0.83[EUR][1000 genomes]
rs12811291	0.83[EUR][1000 genomes]
rs12821454	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12823506	0.85[EUR][1000 genomes]
rs12828340	0.82[EUR][1000 genomes]
rs12832940	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1362983	0.82[EUR][1000 genomes]
rs17124562	0.83[EUR][1000 genomes]
rs1972611	0.84[EUR][1000 genomes]
rs2111988	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2302900	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2358539	0.82[EUR][1000 genomes]
rs28628775	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34039674	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34614542	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34825838	0.82[EUR][1000 genomes]
rs34849043	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34858415	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34894919	0.81[AMR][1000 genomes]
rs35209607	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35535298	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35768991	0.86[EUR][1000 genomes]
rs35878271	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35933908	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3812825	0.83[EUR][1000 genomes]
rs3861100	0.80[EUR][1000 genomes]
rs4768872	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4768949	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4768951	0.85[EUR][1000 genomes]
rs6580735	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6580736	0.85[EUR][1000 genomes]
rs6580737	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6580738	0.85[EUR][1000 genomes]
rs6580739	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6580740	0.87[EUR][1000 genomes]
rs6580741	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67138019	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7132551	0.83[EUR][1000 genomes]
rs7135777	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71465002	0.83[EUR][1000 genomes]
rs7301186	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7301189	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7304445	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7305995	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7308095	0.80[EUR][1000 genomes]
rs7308885	0.83[EUR][1000 genomes]
rs7310541	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7311378	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7311491	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7311973	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7314465	0.82[EUR][1000 genomes]
rs7315871	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7315955	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7399343	0.86[EUR][1000 genomes]
rs7485486	0.82[EUR][1000 genomes]
rs7486747	0.85[EUR][1000 genomes]
rs7488682	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7489214	0.86[EUR][1000 genomes]
rs7953953	0.84[EUR][1000 genomes]
rs7956468	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7974648	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7979830	0.82[EUR][1000 genomes]
rs7980911	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9705460	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
3	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
4	nsv1035796	chr12:50634342-50784312	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv702	chr12:50670870-50715934	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv1053667	chr12:50679039-50801752	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
7	nsv1054480	chr12:50691039-50859665	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv1041563	chr12:50705715-50861699	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	nsv1049665	chr12:50705715-50871542	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs35663729	CERS5	cis	Nerve Tibial	GTEx
rs35663729	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs35663729	ATF1	cis	Artery Tibial	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50690000-50711800	Weak transcription	Ovary	ovary
2	chr12:50692000-50719800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:50693600-50722800	Weak transcription	Fetal Intestine Small	intestine
4	chr12:50706400-50720000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:50706800-50709000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:50707400-50720000	Weak transcription	Osteobl	bone
7	chr12:50707400-50720400	Weak transcription	Stomach Mucosa	stomach
8	chr12:50707600-50719600	Weak transcription	A549	lung
9	chr12:50708600-50709000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:50708600-50709000	Enhancers	Liver	Liver
11	chr12:50708600-50709200	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr12:50708600-50710000	Enhancers	Hela-S3	cervix
13	chr12:50708800-50709000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:50708800-50709000	Enhancers	Muscle Satellite Cultured Cells	--
15	chr12:50708800-50709000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:50708800-50709000	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr12:50708800-50709000	Enhancers	HMEC	breast
18	chr12:50708800-50709000	Enhancers	HSMMtube	muscle
19	chr12:50708800-50709000	Enhancers	NHLF	lung
20	chr12:50708800-50709200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:50708800-50709200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:50708800-50709200	Enhancers	NHDF-Ad	bronchial
23	chr12:50708800-50709400	Enhancers	Rectal Mucosa Donor 31	rectum

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