Variant report

Variant	rs7990344
Chromosome Location	chr13:80059080-80059081
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	NR3C1	chr13:80059070-80059630	A549	lung:	n/a	n/a
2	RCOR1	chr13:80058976-80059978	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr13:80058401-80060319	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr13:80059016-80059628	MCF10A-Er-Src	breast:	n/a	n/a
5	CEBPB	chr13:80059044-80059802	A549	lung:	n/a	n/a
6	STAT3	chr13:80058996-80059590	MCF10A-Er-Src	breast:	n/a	chr13:80059487-80059498
7	SP1	chr13:80058925-80059646	A549	lung:	n/a	n/a
8	FOSL2	chr13:80059012-80059719	A549	lung:	n/a	n/a
9	POLR2A	chr13:80059050-80059598	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr13:80059000-80059624	Hela-S3	cervix:	n/a	n/a
11	FOS	chr13:80059015-80059952	MCF10A-Er-Src	breast:	n/a	n/a
12	NR3C1	chr13:80059030-80059761	A549	lung:	n/a	n/a
13	MYC	chr13:80058597-80059952	MCF10A-Er-Src	breast:	n/a	n/a
14	TCF7L2	chr13:80059050-80060060	Hela-S3	cervix:	n/a	chr13:80059691-80059707 chr13:80059694-80059703 chr13:80059692-80059706 chr13:80059695-80059705
15	E2F4	chr13:80058900-80059515	MCF10A-Er-Src	breast:	n/a	n/a
16	RFX5	chr13:80058960-80059918	Hela-S3	cervix:	n/a	n/a
17	MAFK	chr13:80059050-80059700	HepG2	liver:	n/a	n/a
18	MAFK	chr13:80059056-80059694	HepG2	liver:	n/a	n/a
19	EP300	chr13:80058881-80059743	A549	lung:	n/a	n/a
20	STAT3	chr13:80059021-80059819	MCF10A-Er-Src	breast:	n/a	chr13:80059487-80059498
21	EP300	chr13:80059048-80060156	Hela-S3	cervix:	n/a	n/a
22	JUND	chr13:80059053-80059664	HepG2	liver:	n/a	n/a
23	BRCA1	chr13:80058879-80059947	Hela-S3	cervix:	n/a	n/a
24	ARID3A	chr13:80059079-80059687	HepG2	liver:	n/a	n/a
25	POLR2A	chr13:80058362-80061635	MCF10A-Er-Src	breast:	n/a	n/a
26	EP300	chr13:80058882-80059687	A549	lung:	n/a	n/a
27	MYC	chr13:80058986-80059892	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr13:80058816-80059894	Hela-S3	cervix:	n/a	n/a
29	MAFF	chr13:80059035-80059686	HepG2	liver:	n/a	n/a
30	TCF12	chr13:80058967-80059689	A549	lung:	n/a	n/a
31	MAFK	chr13:80059029-80059693	IMR90	lung:	n/a	n/a
32	STAT3	chr13:80059064-80059588	MCF10A-Er-Src	breast:	n/a	chr13:80059487-80059498
33	FOS	chr13:80058981-80059968	MCF10A-Er-Src	breast:	n/a	n/a
34	FOXA2	chr13:80059001-80059606	A549	lung:	n/a	chr13:80059381-80059393
35	SP1	chr13:80058915-80059764	A549	lung:	n/a	n/a
36	CEBPB	chr13:80059000-80059984	Hela-S3	cervix:	n/a	n/a
37	TEAD4	chr13:80058944-80059662	HepG2	liver:	n/a	n/a
38	TEAD4	chr13:80059018-80059619	ECC-1	luminal epithelium:	n/a	n/a
39	GATA3	chr13:80058874-80059737	A549	lung:	n/a	n/a
40	NR3C1	chr13:80059046-80059731	A549	lung:	n/a	n/a
41	CEBPB	chr13:80059052-80059948	IMR90	lung:	n/a	n/a
42	TBP	chr13:80059075-80059930	Hela-S3	cervix:	n/a	n/a
43	MAFK	chr13:80059059-80060091	Hela-S3	cervix:	n/a	n/a
44	STAT3	chr13:80058973-80059812	MCF10A-Er-Src	breast:	n/a	chr13:80059487-80059498
45	FOS	chr13:80059035-80059855	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:80054400..80056939-chr13:80057406..80059171,2	MCF-7	breast:
2	chr13:80057193..80059999-chr13:80114272..80116741,2	K562	blood:

Variant related genes	Relation type
NDFIP2-AS1	TF binding region
ENSG00000232132	Chromatin interaction
ENSG00000102471	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1208049	0.86[ASN][1000 genomes]
rs1212082	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1335368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1335370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1408049	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1414155	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1414156	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1475797	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1577416	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1577418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1748761	0.86[JPT][hapmap]
rs1853830	0.86[JPT][hapmap]
rs2065743	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2181433	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2265377	0.92[JPT][hapmap]
rs2265378	0.86[JPT][hapmap]
rs2476173	0.89[ASN][1000 genomes]
rs2484343	0.89[ASN][1000 genomes]
rs2484344	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2760101	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2760102	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2760103	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2760105	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2760106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2763809	0.86[JPT][hapmap]
rs2763810	0.86[JPT][hapmap]
rs2783119	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2783120	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2783121	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2783122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2783125	0.81[ASN][1000 genomes]
rs2783126	0.81[ASN][1000 genomes]
rs2783127	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2876740	0.86[JPT][hapmap]
rs314687	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs314688	0.85[ASN][1000 genomes]
rs314689	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3742117	0.80[CHB][hapmap]
rs386603	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4145207	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4476060	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4885633	0.88[ASN][1000 genomes]
rs4885634	0.93[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs4885636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs643778	0.86[JPT][hapmap]
rs6563110	0.94[ASN][1000 genomes]
rs6563113	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6563115	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6563116	0.91[ASN][1000 genomes]
rs700396	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7321953	0.92[ASN][1000 genomes]
rs73235963	0.89[ASN][1000 genomes]
rs7325095	0.84[ASN][1000 genomes]
rs7328494	0.92[JPT][hapmap]
rs7338530	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7339303	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7982263	0.95[ASN][1000 genomes]
rs7987193	0.86[JPT][hapmap]
rs7988601	0.94[ASN][1000 genomes]
rs7990250	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7996493	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8001281	0.86[JPT][hapmap]
rs8002042	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs912639	0.86[JPT][hapmap]
rs9318640	0.85[JPT][hapmap]
rs9318641	0.85[JPT][hapmap]
rs9318644	0.92[ASN][1000 genomes]
rs9530922	0.88[ASN][1000 genomes]
rs9530925	0.96[ASN][1000 genomes]
rs9545097	0.85[JPT][hapmap]
rs9565497	0.86[JPT][hapmap]
rs9565510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9574422	0.86[JPT][hapmap]
rs9574429	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9574434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9593399	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9601240	0.89[ASN][1000 genomes]
rs9601242	0.89[ASN][1000 genomes]
rs987284	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv832657	chr13:79904978-80099108	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv523979	chr13:79979679-80120263	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7990344	RBM26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:80054800-80059400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr13:80056200-80059200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr13:80056200-80060600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr13:80056200-80060800	Weak transcription	Gastric	stomach
5	chr13:80056200-80063200	Weak transcription	Left Ventricle	heart
6	chr13:80056200-80066400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr13:80056200-80066600	Weak transcription	Psoas Muscle	Psoas
8	chr13:80056200-80077400	Weak transcription	Right Ventricle	heart
9	chr13:80056600-80064200	Weak transcription	Placenta	Placenta
10	chr13:80056800-80059200	Weak transcription	Pancreas	Pancrea
11	chr13:80056800-80059600	Enhancers	Brain Hippocampus Middle	brain
12	chr13:80056800-80059600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr13:80056800-80061200	Enhancers	Fetal Heart	heart
14	chr13:80056800-80064000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr13:80056800-80064400	Weak transcription	Fetal Stomach	stomach
16	chr13:80056800-80065800	Weak transcription	Fetal Muscle Leg	muscle
17	chr13:80057000-80059200	Enhancers	HepG2	liver
18	chr13:80057000-80063600	Weak transcription	Right Atrium	heart
19	chr13:80057000-80066200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr13:80057200-80059200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr13:80057200-80060600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr13:80057400-80059200	Weak transcription	Esophagus	oesophagus
23	chr13:80057400-80060800	Enhancers	HSMM	muscle
24	chr13:80057400-80063400	Weak transcription	GM12878-XiMat	blood
25	chr13:80057400-80064600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr13:80057600-80059200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr13:80057600-80059200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr13:80057600-80059200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr13:80057600-80059200	Weak transcription	Colon Smooth Muscle	Colon
30	chr13:80057600-80059200	Weak transcription	Fetal Lung	lung
31	chr13:80057600-80060000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr13:80057600-80061000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr13:80057600-80065400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr13:80057600-80065600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr13:80057800-80059200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr13:80057800-80059200	Weak transcription	Brain Angular Gyrus	brain
37	chr13:80057800-80059200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr13:80057800-80064600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr13:80057800-80064600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr13:80058000-80059200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr13:80058000-80059200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr13:80058000-80059200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr13:80058000-80059400	Weak transcription	Brain Anterior Caudate	brain
44	chr13:80058000-80059400	Enhancers	HMEC	breast
45	chr13:80058000-80059400	Enhancers	NH-A	brain
46	chr13:80058000-80059400	Enhancers	Osteobl	bone
47	chr13:80058000-80060200	Enhancers	Muscle Satellite Cultured Cells	--
48	chr13:80058000-80065400	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr13:80058200-80059200	Enhancers	Fetal Intestine Large	intestine
50	chr13:80058200-80059800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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