Variant report

Variant	rs13387836
Chromosome Location	chr2:55278559-55278560
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	TCF12	chr2:55277108-55278970	SK-N-SH	brain:	n/a	chr2:55277949-55277956 chr2:55278509-55278518
2	JUND	chr2:55278209-55278693	HepG2	liver:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55278402-55278411 chr2:55278401-55278411 chr2:55278401-55278411 chr2:55278400-55278411
3	FOSL1	chr2:55278181-55278739	K562	blood:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55278402-55278411 chr2:55278400-55278411 chr2:55278401-55278411 chr2:55278401-55278411
4	MAFK	chr2:55278287-55278822	HepG2	liver:	n/a	chr2:55278509-55278518
5	RXRA	chr2:55278157-55278728	SK-N-SH	brain:	n/a	n/a
6	MAX	chr2:55277384-55278893	A549	lung:	n/a	chr2:55278420-55278430
7	TEAD4	chr2:55277123-55278992	K562	blood:	n/a	n/a
8	TAF1	chr2:55277170-55278561	K562	blood:	n/a	n/a
9	GABPA	chr2:55277388-55278643	MCF-7	breast:	n/a	n/a
10	BCL3	chr2:55277282-55278900	A549	lung:	n/a	chr2:55277604-55277613 chr2:55277645-55277654 chr2:55278055-55278064
11	POLR2A	chr2:55275958-55278821	HUVEC	blood vessel:	n/a	n/a
12	UBTF	chr2:55274752-55278735	K562	blood:	n/a	n/a
13	SMARCC1	chr2:55277068-55278785	Hela-S3	cervix:	n/a	chr2:55278402-55278411 chr2:55277702-55277711
14	POLR2A	chr2:55277116-55278826	PBDE	blood:	n/a	n/a
15	POLR2A	chr2:55276933-55278685	K562	blood:	n/a	n/a
16	NR2F2	chr2:55277170-55278978	K562	blood:	n/a	n/a
17	POLR2A	chr2:55275602-55278945	HCT-116	colon:	n/a	n/a
18	STAT3	chr2:55278274-55278791	MCF10A-Er-Src	breast:	n/a	chr2:55278443-55278450
19	REST	chr2:55278326-55278601	K562	blood:	n/a	n/a
20	ATF3	chr2:55278147-55278717	K562	blood:	n/a	n/a
21	SIN3A	chr2:55275650-55278654	H1-hESC	embryonic stem cell:	n/a	chr2:55276189-55276200
22	RCOR1	chr2:55275614-55278876	Hela-S3	cervix:	n/a	n/a
23	BRCA1	chr2:55277481-55279097	Hela-S3	cervix:	n/a	chr2:55277795-55277802
24	POLR2A	chr2:55277242-55278783	HUVEC	blood vessel:	n/a	n/a
25	JUN	chr2:55278209-55278680	K562	blood:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55278402-55278411 chr2:55278401-55278411 chr2:55278401-55278411
26	JUND	chr2:55278109-55278795	A549	lung:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55278402-55278411 chr2:55278401-55278411 chr2:55278401-55278411 chr2:55278400-55278411
27	RUNX3	chr2:55277173-55278605	GM12878	blood:	n/a	chr2:55278265-55278280
28	POLR2A	chr2:55277032-55278781	PANC-1	pancreas:	n/a	n/a
29	SIN3AK20	chr2:55277897-55278908	A549	lung:	n/a	n/a
30	FOSL2	chr2:55278094-55278782	MCF-7	breast:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55278401-55278412 chr2:55278402-55278411 chr2:55278401-55278411 chr2:55278401-55278411
31	MTA3	chr2:55277082-55278821	GM12878	blood:	n/a	n/a
32	MAFK	chr2:55278216-55278984	Hela-S3	cervix:	n/a	chr2:55278509-55278518
33	MEF2A	chr2:55278137-55278869	SK-N-SH	brain:	n/a	chr2:55278139-55278154
34	TEAD4	chr2:55278217-55278923	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr2:55275829-55278945	SK-N-MC	brain:	n/a	n/a
36	BHLHE40	chr2:55277381-55278618	HepG2	liver:	n/a	n/a
37	MYBL2	chr2:55277192-55278721	HepG2	liver:	n/a	n/a
38	FOSL2	chr2:55278186-55278655	HepG2	liver:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55278401-55278412 chr2:55278402-55278411 chr2:55278401-55278411 chr2:55278401-55278411
39	TCF12	chr2:55277846-55278828	A549	lung:	n/a	chr2:55277949-55277956 chr2:55278509-55278518
40	TCF12	chr2:55275501-55278974	A549	lung:	n/a	chr2:55277949-55277956 chr2:55275946-55275954 chr2:55278509-55278518
41	BACH1	chr2:55277603-55278725	H1-hESC	embryonic stem cell:	n/a	chr2:55277699-55277713
42	RXRA	chr2:55277975-55278933	SK-N-SH	brain:	n/a	chr2:55278024-55278044
43	MXI1	chr2:55275607-55278907	IMR90	lung:	n/a	n/a
44	MAX	chr2:55277085-55278950	A549	lung:	n/a	chr2:55278420-55278430
45	YY1	chr2:55278255-55278617	HCT-116	colon:	n/a	n/a
46	HEY1	chr2:55276951-55278619	K562	blood:	n/a	n/a
47	POLR2A	chr2:55278230-55278580	ECC-1	luminal epithelium:	n/a	n/a
48	TEAD4	chr2:55277956-55278925	SK-N-SH	brain:	n/a	n/a
49	TAF1	chr2:55278217-55278717	SK-N-SH	brain:	n/a	n/a
50	JUN	chr2:55275513-55278923	K562	blood:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55278402-55278411 chr2:55278401-55278411 chr2:55277702-55277711 chr2:55278401-55278411

No.	Distal block	Cell Line	Cell type
1	chr2:55276798..55279791-chr2:55841794..55843892,2	K562	blood:
2	chr2:55278226..55280278-chr2:55389625..55391199,2	MCF-7	breast:
3	chr2:55273237..55280299-chr2:55335301..55344768,18	K562	blood:
4	chr2:55275304..55279887-chr2:55458370..55461390,5	K562	blood:
5	chr2:55278214..55278967-chr2:88926117..88926888,2	Hela-S3	cervix:
6	chr2:55278333..55279964-chr2:55343174..55345064,2	MCF-7	breast:
7	chr2:55276121..55279274-chr2:55457448..55460901,6	K562	blood:
8	chr2:55273237..55279836-chr2:55336432..55344363,17	K562	blood:
9	chr2:55278300..55281080-chr2:55325086..55327233,3	K562	blood:
10	chr2:55276251..55278794-chr2:55450594..55452106,2	MCF-7	breast:

Variant related genes	Relation type
RTN4	TF binding region
ENSG00000115310	Chromatin interaction
ENSG00000162994	Chromatin interaction
ENSG00000138041	Chromatin interaction
ENSG00000143947	Chromatin interaction
ENSG00000266376	Chromatin interaction
ENSG00000227799	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10173203	0.87[EUR][1000 genomes]
rs3198123	0.82[EUR][1000 genomes]
rs6545469	0.81[AFR][1000 genomes]
rs6760379	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601895	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55272400-55279600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:55273400-55279800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:55273800-55278600	Active TSS	H1 Cell Line	embryonic stem cell
4	chr2:55273800-55278600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:55273800-55279000	Active TSS	Psoas Muscle	Psoas
6	chr2:55273800-55279200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:55274200-55278600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:55274200-55278600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:55274200-55279000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:55274200-55279200	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr2:55274200-55279600	Active TSS	HMEC	breast
12	chr2:55274400-55278800	Active TSS	Fetal Brain Male	brain
13	chr2:55274600-55278600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:55274600-55278600	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr2:55274600-55278800	Active TSS	Aorta	Aorta
16	chr2:55274600-55278800	Active TSS	Fetal Muscle Trunk	muscle
17	chr2:55274600-55279200	Active TSS	NHEK	skin
18	chr2:55274800-55278600	Active TSS	Hela-S3	cervix
19	chr2:55274800-55278800	Active TSS	Ovary	ovary
20	chr2:55274800-55279000	Active TSS	H9 Cell Line	embryonic stem cell
21	chr2:55274800-55279000	Active TSS	Right Ventricle	heart
22	chr2:55275000-55278600	Active TSS	Colonic Mucosa	Colon
23	chr2:55275000-55278800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:55275000-55278800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:55275000-55279400	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr2:55275000-55279400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:55275200-55278600	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr2:55275200-55278600	Active TSS	Placenta Amnion	Placenta Amnion
29	chr2:55275200-55278600	Active TSS	Stomach Mucosa	stomach
30	chr2:55275200-55278800	Active TSS	Left Ventricle	heart
31	chr2:55275200-55279200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:55275400-55278600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:55275400-55278600	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr2:55275400-55278600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:55275400-55278600	Active TSS	Esophagus	oesophagus
36	chr2:55275400-55278600	Active TSS	Gastric	stomach
37	chr2:55275400-55278600	Active TSS	Pancreas	Pancrea
38	chr2:55275400-55278600	Active TSS	HUVEC	blood vessel
39	chr2:55275400-55278600	Active TSS	NHDF-Ad	bronchial
40	chr2:55275400-55278800	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr2:55275400-55279000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:55275400-55279600	Active TSS	A549	lung
43	chr2:55275600-55278800	Active TSS	HSMM	muscle
44	chr2:55275800-55279200	Active TSS	Thymus	Thymus
45	chr2:55275800-55280000	Active TSS	NHLF	lung
46	chr2:55276000-55278600	Bivalent/Poised TSS	HepG2	liver
47	chr2:55276200-55279200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:55277400-55279000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:55277400-55279200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:55277800-55279000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links