Variant report

Variant	rs976654
Chromosome Location	chr4:102898570-102898571
allele	G/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	EP300	chr4:102898077-102898814	ECC-1	luminal epithelium:	n/a	n/a
2	GTF2F1	chr4:102898136-102898629	Hela-S3	cervix:	n/a	n/a
3	SP1	chr4:102898050-102898801	A549	lung:	n/a	chr4:102898697-102898718
4	FOSL1	chr4:102898072-102898703	HCT-116	colon:	n/a	n/a
5	FOSL2	chr4:102898171-102898630	A549	lung:	n/a	n/a
6	USF1	chr4:102898240-102898597	A549	lung:	n/a	n/a
7	MAX	chr4:102898315-102898617	A549	lung:	n/a	n/a
8	E2F4	chr4:102898327-102898604	MCF10A-Er-Src	breast:	n/a	n/a
9	JUND	chr4:102898248-102898745	A549	lung:	n/a	n/a
10	SIN3AK20	chr4:102898256-102898585	SK-N-SH	brain:	n/a	n/a
11	TCF12	chr4:102898145-102898713	ECC-1	luminal epithelium:	n/a	n/a
12	PBX3	chr4:102898080-102898741	SK-N-SH	brain:	n/a	n/a
13	CEBPB	chr4:102898283-102898601	ECC-1	luminal epithelium:	n/a	n/a
14	EP300	chr4:102898168-102898745	Hela-S3	cervix:	n/a	n/a
15	BRCA1	chr4:102897789-102898772	Hela-S3	cervix:	n/a	n/a
16	SMC3	chr4:102898231-102898628	Hela-S3	cervix:	n/a	n/a
17	SP1	chr4:102898059-102898786	HCT-116	colon:	n/a	chr4:102898697-102898718
18	MYC	chr4:102898115-102898881	A549	lung:	n/a	n/a
19	ELK1	chr4:102898334-102898614	Hela-S3	cervix:	n/a	n/a
20	FOSL2	chr4:102898171-102898688	SK-N-SH	brain:	n/a	n/a
21	CEBPB	chr4:102898157-102898779	HCT-116	colon:	n/a	n/a
22	PRDM1	chr4:102898333-102898591	Hela-S3	cervix:	n/a	chr4:102898420-102898435
23	TCF12	chr4:102898038-102898913	A549	lung:	n/a	n/a
24	FOSL2	chr4:102898001-102899075	SK-N-SH	brain:	n/a	chr4:102899021-102899029 chr4:102898907-102898917 chr4:102898907-102898917 chr4:102898908-102898917 chr4:102898907-102898917 chr4:102898907-102898917
25	TCF12	chr4:102897888-102899039	SK-N-SH	brain:	n/a	n/a
26	MAZ	chr4:102898191-102898692	Hela-S3	cervix:	n/a	n/a
27	MAX	chr4:102898080-102898857	A549	lung:	n/a	n/a
28	CEBPB	chr4:102898018-102898966	Hela-S3	cervix:	n/a	n/a
29	RCOR1	chr4:102898149-102898781	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr4:102898236-102898582	HCT-116	colon:	n/a	n/a
31	STAT3	chr4:102898231-102898967	MCF10A-Er-Src	breast:	n/a	chr4:102898763-102898770 chr4:102898908-102898917
32	FOSL1	chr4:102898127-102898750	HCT-116	colon:	n/a	n/a
33	MAX	chr4:102898071-102898783	HCT-116	colon:	n/a	n/a
34	JUN	chr4:102898204-102898716	Hela-S3	cervix:	n/a	n/a
35	TEAD4	chr4:102898118-102898730	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr4:102898139-102898649	SK-N-SH	brain:	n/a	n/a
37	EP300	chr4:102898072-102898925	A549	lung:	n/a	chr4:102898907-102898916
38	EP300	chr4:102897997-102898903	A549	lung:	n/a	n/a
39	POLR2A	chr4:102898145-102898628	HUVEC	blood vessel:	n/a	n/a
40	EP300	chr4:102898296-102898705	ECC-1	luminal epithelium:	n/a	n/a
41	MAX	chr4:102898187-102898780	A549	lung:	n/a	n/a
42	SP1	chr4:102898104-102898892	A549	lung:	n/a	chr4:102898697-102898718
43	SRF	chr4:102898139-102898826	HCT-116	colon:	n/a	n/a
44	JUND	chr4:102898175-102898653	A549	lung:	n/a	n/a
45	STAT3	chr4:102898106-102898656	MCF10A-Er-Src	breast:	n/a	n/a
46	MYC	chr4:102898127-102898893	MCF10A-Er-Src	breast:	n/a	n/a
47	CBX3	chr4:102898123-102898750	HCT-116	colon:	n/a	n/a
48	SIN3AK20	chr4:102898172-102898762	HCT-116	colon:	n/a	n/a
49	MYC	chr4:102898229-102898654	MCF10A-Er-Src	breast:	n/a	n/a
50	PBX3	chr4:102897996-102898821	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
BANK1	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1027013	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1352174	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1386173	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1386176	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1486572	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1843680	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2631244	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2631246	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2631249	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2850375	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2850377	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2850378	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2850379	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2850383	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2850387	0.82[EUR][1000 genomes]
rs2851319	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2851320	0.85[EUR][1000 genomes]
rs2851328	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2851329	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2851333	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2851334	0.85[EUR][1000 genomes]
rs2851336	0.89[EUR][1000 genomes]
rs901406	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs923206	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs923207	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869164	chr4:102483189-103213842	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv999861	chr4:102576115-102930562	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv2757945	chr4:102662699-103008940	Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2759269	chr4:102662699-103008940	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1011180	chr4:102685236-102985945	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv537202	chr4:102685236-102985945	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv2757074	chr4:102772861-102933949	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv879682	chr4:102859835-103088491	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs976654	BANK1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102894000-102905200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr4:102894200-102900600	Strong transcription	Primary B cells from peripheral blood	blood
3	chr4:102896400-102898600	Enhancers	A549	lung
4	chr4:102896600-102898800	Strong transcription	Primary B cells from cord blood	blood
5	chr4:102896600-102899200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr4:102896600-102899800	Enhancers	Hela-S3	cervix
7	chr4:102897200-102898600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:102897200-102899200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:102897600-102899000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:102897600-102899200	Enhancers	HUVEC	blood vessel
11	chr4:102897800-102898800	Enhancers	HSMM	muscle
12	chr4:102897800-102899000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:102897800-102899000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:102897800-102899000	Enhancers	Muscle Satellite Cultured Cells	--
15	chr4:102897800-102899000	Enhancers	NH-A	brain
16	chr4:102897800-102899000	Enhancers	NHEK	skin
17	chr4:102897800-102899000	Enhancers	Osteobl	bone
18	chr4:102898000-102898600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:102898000-102898800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:102898000-102898800	Enhancers	HMEC	breast
21	chr4:102898000-102898800	Enhancers	NHDF-Ad	bronchial
22	chr4:102898200-102898800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:102898200-102898800	Enhancers	HSMMtube	muscle

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