Variant report

Variant	rs67156582
Chromosome Location	chr2:55240599-55240600
allele	A/C
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	POLR2A	chr2:55240509-55240669	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr2:55222320-55241658	K562	blood:	n/a	n/a
3	POLR2A	chr2:55240589-55240607	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr2:55238935-55240618	SK-N-SH	brain:	n/a	n/a
5	HNF4A	chr2:55240230-55240603	HepG2	liver:	n/a	chr2:55240407-55240420 chr2:55240408-55240420 chr2:55240407-55240422 chr2:55240407-55240421 chr2:55240408-55240421 chr2:55240407-55240420 chr2:55240407-55240420 chr2:55240409-55240421 chr2:55240407-55240422 chr2:55240407-55240421 chr2:55240405-55240423 chr2:55240408-55240420 chr2:55240406-55240421 chr2:55240407-55240422 chr2:55240408-55240420
6	CEBPB	chr2:55240258-55240602	HepG2	liver:	n/a	chr2:55240420-55240431
7	POLR2A	chr2:55239038-55240752	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55238547..55240641-chr2:55252176..55254092,2	MCF-7	breast:
2	chr2:55239250..55241157-chr2:55276968..55279206,2	K562	blood:
3	chr2:55239258..55241140-chr2:55243082..55244742,2	K562	blood:
4	chr2:55236989..55239116-chr2:55240470..55242602,2	K562	blood:

Variant related genes	Relation type
RTN4	TF binding region
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10170340	0.93[ASN][1000 genomes]
rs10189379	0.82[ASN][1000 genomes]
rs12464447	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12464595	0.81[ASN][1000 genomes]
rs12469804	0.85[ASN][1000 genomes]
rs12475787	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12475904	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17046570	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17046594	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17347089	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17418675	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2289747	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2864049	0.94[ASN][1000 genomes]
rs55659423	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55698303	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55762835	0.84[ASN][1000 genomes]
rs55993793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56013263	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6707036	0.85[EUR][1000 genomes]
rs6713935	0.82[ASN][1000 genomes]
rs6722182	0.82[ASN][1000 genomes]
rs72795431	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72795440	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7582359	0.85[EUR][1000 genomes]
rs7601625	0.85[ASN][1000 genomes]
rs887	0.82[EUR][1000 genomes];0.90[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	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	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:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
2	chr2:55232200-55244800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:55234800-55244800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:55234800-55246000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:55235600-55240600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:55236600-55241400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr2:55236800-55240800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:55236800-55243400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr2:55237000-55243600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr2:55237200-55241600	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr2:55237400-55240800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr2:55237400-55242800	Enhancers	HSMMtube	muscle
13	chr2:55237600-55240800	Enhancers	Colon Smooth Muscle	Colon
14	chr2:55237600-55241000	Enhancers	NH-A	brain
15	chr2:55237600-55241200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:55237600-55241400	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr2:55237600-55241400	Enhancers	Fetal Lung	lung
18	chr2:55237600-55241600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr2:55237600-55242000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr2:55237600-55243600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:55237600-55246000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:55237600-55247800	Weak transcription	Left Ventricle	heart
23	chr2:55237600-55249600	Weak transcription	Gastric	stomach
24	chr2:55237600-55250200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:55237600-55258600	Weak transcription	Ovary	ovary
26	chr2:55237600-55272600	Weak transcription	Fetal Stomach	stomach
27	chr2:55237800-55240600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr2:55237800-55241000	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr2:55237800-55241000	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr2:55237800-55241000	Enhancers	Brain Cingulate Gyrus	brain
31	chr2:55237800-55241200	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr2:55237800-55241200	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr2:55237800-55241200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:55237800-55241200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:55237800-55241600	Enhancers	Duodenum Mucosa	Duodenum
36	chr2:55237800-55242200	Enhancers	NHLF	lung
37	chr2:55237800-55242800	Enhancers	Brain Substantia Nigra	brain
38	chr2:55237800-55242800	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr2:55237800-55242800	Enhancers	Rectal Smooth Muscle	rectum
40	chr2:55237800-55243000	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr2:55237800-55243400	Enhancers	Osteobl	bone
42	chr2:55237800-55243600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:55237800-55243600	Enhancers	Brain Hippocampus Middle	brain
44	chr2:55238000-55241000	Enhancers	Primary hematopoietic stem cells	blood
45	chr2:55238000-55241200	Enhancers	GM12878-XiMat	blood
46	chr2:55238000-55241400	Enhancers	Primary T cells from cord blood	blood
47	chr2:55238000-55241400	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr2:55238000-55243000	Enhancers	Adipose Nuclei	Adipose
49	chr2:55238200-55240600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:55238200-55245800	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links