Variant report

Variant	rs13008890
Chromosome Location	chr2:67487964-67487965
allele	A/G
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	FOSL2	chr2:67487648-67488580	A549	lung:	n/a	chr2:67488550-67488559
2	FOS	chr2:67487668-67488460	MCF10A-Er-Src	breast:	n/a	n/a
3	TEAD4	chr2:67486524-67488583	SK-N-SH	brain:	n/a	n/a
4	JUND	chr2:67486530-67488629	SK-N-SH	brain:	n/a	chr2:67486779-67486790 chr2:67488550-67488559
5	POLR2A	chr2:67486781-67489256	MCF10A-Er-Src	breast:	n/a	n/a
6	EP300	chr2:67487903-67488562	ECC-1	luminal epithelium:	n/a	chr2:67488548-67488562
7	TEAD4	chr2:67487797-67488492	ECC-1	luminal epithelium:	n/a	n/a
8	CHD2	chr2:67487812-67488438	Hela-S3	cervix:	n/a	n/a
9	CEBPB	chr2:67487809-67488310	A549	lung:	n/a	n/a
10	NFIC	chr2:67487725-67488541	ECC-1	luminal epithelium:	n/a	chr2:67487785-67487813
11	POLR2A	chr2:67487791-67488477	Hela-S3	cervix:	n/a	n/a
12	MAFK	chr2:67486669-67488670	Hela-S3	cervix:	n/a	n/a
13	EP300	chr2:67487768-67488409	A549	lung:	n/a	n/a
14	TCF12	chr2:67487813-67488502	ECC-1	luminal epithelium:	n/a	n/a
15	NFIC	chr2:67487675-67488517	SK-N-SH	brain:	n/a	chr2:67487785-67487813
16	RFX5	chr2:67487930-67488463	Hela-S3	cervix:	n/a	n/a
17	MAFK	chr2:67486659-67488612	IMR90	lung:	n/a	n/a
18	TCF12	chr2:67486498-67488668	SK-N-SH	brain:	n/a	n/a
19	EP300	chr2:67486172-67488638	SK-N-SH	brain:	n/a	chr2:67488548-67488562 chr2:67488582-67488596 chr2:67486858-67486872
20	EP300	chr2:67487822-67488436	Hela-S3	cervix:	n/a	n/a
21	MEF2A	chr2:67487679-67488607	SK-N-SH	brain:	n/a	chr2:67487741-67487756 chr2:67487741-67487757
22	EP300	chr2:67487597-67488647	ECC-1	luminal epithelium:	n/a	chr2:67488548-67488562 chr2:67488582-67488596
23	RAD21	chr2:67487794-67488515	Hela-S3	cervix:	n/a	n/a
24	NFIC	chr2:67487691-67488598	ECC-1	luminal epithelium:	n/a	chr2:67487785-67487813
25	NFIC	chr2:67486447-67488598	SK-N-SH	brain:	n/a	chr2:67487785-67487813
26	SP1	chr2:67487862-67488453	A549	lung:	n/a	n/a
27	FOSL2	chr2:67486542-67488574	SK-N-SH	brain:	n/a	chr2:67486779-67486790 chr2:67488550-67488559
28	STAT3	chr2:67487736-67488449	MCF10A-Er-Src	breast:	n/a	n/a
29	FOSL2	chr2:67487838-67488348	SK-N-SH	brain:	n/a	n/a
30	TBP	chr2:67487792-67488763	Hela-S3	cervix:	n/a	n/a
31	TCF12	chr2:67486476-67488686	SK-N-SH	brain:	n/a	n/a
32	GATA3	chr2:67487819-67488677	A549	lung:	n/a	chr2:67488605-67488615
33	SMC3	chr2:67487588-67488469	Hela-S3	cervix:	n/a	n/a
34	EP300	chr2:67487800-67488459	A549	lung:	n/a	n/a
35	FOS	chr2:67487679-67488524	MCF10A-Er-Src	breast:	n/a	n/a
36	MAX	chr2:67487592-67488496	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr2:67487812-67488490	SK-N-SH	brain:	n/a	n/a
38	FOSL2	chr2:67487907-67488258	A549	lung:	n/a	n/a
39	FOXM1	chr2:67487766-67488580	ECC-1	luminal epithelium:	n/a	n/a
40	STAT3	chr2:67487740-67488395	MCF10A-Er-Src	breast:	n/a	n/a
41	TCF12	chr2:67487756-67488632	ECC-1	luminal epithelium:	n/a	n/a
42	CEBPB	chr2:67487734-67488440	Hela-S3	cervix:	n/a	n/a
43	BRCA1	chr2:67487883-67488847	Hela-S3	cervix:	n/a	n/a
44	TEAD4	chr2:67487728-67488645	SK-N-SH	brain:	n/a	n/a
45	STAT3	chr2:67487899-67488351	Hela-S3	cervix:	n/a	n/a
46	FOXM1	chr2:67486470-67488539	SK-N-SH	brain:	n/a	n/a
47	GTF2F1	chr2:67486765-67488530	Hela-S3	cervix:	n/a	n/a
48	RXRA	chr2:67487583-67488600	SK-N-SH	brain:	n/a	n/a
49	EP300	chr2:67487848-67488358	SK-N-SH_RA	brain:	n/a	n/a
50	MYC	chr2:67487869-67488425	MCF10A-Er-Src	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ETAA1-5	chr2:67487935-67488339	XLOC_001512

Variant related genes	Relation type
ENSG00000235885	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10496153	1.00[MEX][hapmap]
rs1063571	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs13015287	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17601386	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34262449	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34286589	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62146349	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6741192	0.83[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008584	chr2:67168244-67703601	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv535775	chr2:67168244-67703601	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv534389	chr2:67388428-68225338	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1001672	chr2:67429146-67498042	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:67482400-67488200	Enhancers	Hela-S3	cervix
2	chr2:67485400-67488800	Enhancers	Fetal Stomach	stomach
3	chr2:67486200-67488200	Enhancers	HUVEC	blood vessel
4	chr2:67486200-67488200	Enhancers	NHLF	lung
5	chr2:67486200-67488400	Enhancers	Rectal Smooth Muscle	rectum
6	chr2:67486200-67488400	Enhancers	HMEC	breast
7	chr2:67486200-67488800	Enhancers	NHEK	skin
8	chr2:67486200-67489000	Enhancers	Colon Smooth Muscle	Colon
9	chr2:67486800-67488200	Enhancers	HSMMtube	muscle
10	chr2:67486800-67488600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:67487000-67488000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:67487000-67488000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr2:67487000-67488000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:67487000-67488000	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr2:67487000-67488000	Flanking Active TSS	NHDF-Ad	bronchial
16	chr2:67487000-67488400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:67487000-67488400	Enhancers	Fetal Muscle Leg	muscle
18	chr2:67487000-67488600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:67487200-67488000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:67487200-67488600	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr2:67487200-67488600	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr2:67487400-67488400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:67487400-67488600	Active TSS	Stomach Smooth Muscle	stomach
24	chr2:67487400-67488800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:67487400-67488800	Active TSS	Aorta	Aorta
26	chr2:67487400-67491400	Weak transcription	Psoas Muscle	Psoas
27	chr2:67487600-67488000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:67487600-67488000	Weak transcription	Ovary	ovary
29	chr2:67487800-67488000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:67487800-67488000	Flanking Active TSS	NH-A	brain
31	chr2:67487800-67488200	Enhancers	Fetal Lung	lung
32	chr2:67487800-67488200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr2:67487800-67488200	Enhancers	HSMM	muscle
34	chr2:67487800-67488200	Enhancers	Osteobl	bone
35	chr2:67487800-67488400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:67487800-67488600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:67487800-67488800	Flanking Active TSS	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links