Variant report

Variant	rs13006159
Chromosome Location	chr2:55341308-55341309
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	chr2:55341260-55341635	HepG2	liver:	n/a	chr2:55341445-55341453 chr2:55341444-55341454 chr2:55341333-55341342 chr2:55341443-55341455
2	RCOR1	chr2:55341298-55341498	K562	blood:	n/a	n/a
3	JUND	chr2:55341197-55341487	HepG2	liver:	n/a	chr2:55341445-55341453 chr2:55341444-55341454 chr2:55341333-55341342 chr2:55341443-55341455
4	MAFK	chr2:55341095-55341549	HepG2	liver:	n/a	chr2:55341264-55341278 chr2:55341261-55341277 chr2:55341265-55341276 chr2:55341212-55341223 chr2:55341266-55341277 chr2:55341446-55341455 chr2:55341265-55341276
5	MAFF	chr2:55341101-55341591	HepG2	liver:	n/a	chr2:55341260-55341278
6	MAFK	chr2:55341106-55341559	HepG2	liver:	n/a	chr2:55341264-55341278 chr2:55341261-55341277 chr2:55341265-55341276 chr2:55341212-55341223 chr2:55341266-55341277 chr2:55341446-55341455 chr2:55341265-55341276
7	RCOR1	chr2:55338384-55341644	IMR90	lung:	n/a	n/a
8	MAFF	chr2:55341255-55341449	K562	blood:	n/a	chr2:55341260-55341278
9	JUND	chr2:55341287-55341530	K562	blood:	n/a	chr2:55341445-55341453 chr2:55341444-55341454 chr2:55341333-55341342 chr2:55341443-55341455
10	MAFK	chr2:55341004-55341499	K562	blood:	n/a	chr2:55341264-55341278 chr2:55341261-55341277 chr2:55341265-55341276 chr2:55341212-55341223 chr2:55341266-55341277 chr2:55341446-55341455 chr2:55341265-55341276
11	STAT3	chr2:55341236-55341417	MCF10A-Er-Src	breast:	n/a	n/a
12	JUN	chr2:55341257-55341457	HepG2	liver:	n/a	chr2:55341445-55341453 chr2:55341329-55341342 chr2:55341444-55341454 chr2:55341333-55341342 chr2:55341443-55341455

No.	Distal block	Cell Line	Cell type
1	chr2:55273237..55280299-chr2:55335301..55344768,18	K562	blood:
2	chr2:55273237..55279836-chr2:55336432..55344363,17	K562	blood:
3	chr2:55339781..55342552-chr2:55346442..55349594,4	K562	blood:

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

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10496039	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11681508	0.92[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs11692696	0.92[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12713287	0.91[ASN][1000 genomes]
rs12988226	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12990261	0.90[ASN][1000 genomes]
rs12992634	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13023960	0.84[AMR][1000 genomes]
rs35885020	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59778045	0.82[AMR][1000 genomes]
rs62138263	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6729033	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004503	chr2:55324276-55343705	Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv997458	chr2:55324276-55344326	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1013316	chr2:55324276-55345262	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55329600-55342600	Weak transcription	NHEK	skin
2	chr2:55332000-55343400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:55337200-55351000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:55337400-55342800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:55337400-55342800	Weak transcription	HMEC	breast
6	chr2:55338400-55343400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr2:55338400-55343400	Enhancers	Primary hematopoietic stem cells	blood
8	chr2:55338600-55341400	Flanking Active TSS	HSMMtube	muscle
9	chr2:55338600-55341400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr2:55338600-55341600	Enhancers	Fetal Thymus	thymus
11	chr2:55338600-55343800	Enhancers	Fetal Muscle Leg	muscle
12	chr2:55339200-55343000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:55339400-55351000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:55339600-55341400	Enhancers	NHDF-Ad	bronchial
15	chr2:55339600-55342200	Weak transcription	Hela-S3	cervix
16	chr2:55339600-55342600	Enhancers	A549	lung
17	chr2:55339600-55345800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:55339600-55345800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr2:55339600-55345800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:55339600-55346800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:55339600-55347000	Weak transcription	Left Ventricle	heart
22	chr2:55339800-55342600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:55339800-55343000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:55339800-55343000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:55339800-55344400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:55339800-55345600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr2:55339800-55345800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:55339800-55347000	Weak transcription	Lung	lung
29	chr2:55340000-55341600	Bivalent Enhancer	HepG2	liver
30	chr2:55340000-55342400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr2:55340000-55343600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:55340000-55343600	Enhancers	NHLF	lung
33	chr2:55340000-55345600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr2:55340200-55342400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:55340200-55342600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:55340200-55343200	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr2:55340200-55346200	Weak transcription	Fetal Brain Female	brain
38	chr2:55340400-55341600	Enhancers	Muscle Satellite Cultured Cells	--
39	chr2:55340400-55341800	Enhancers	Gastric	stomach
40	chr2:55340400-55342600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:55340400-55343000	Weak transcription	Small Intestine	intestine
42	chr2:55340400-55344200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr2:55340400-55345800	Enhancers	K562	blood
44	chr2:55340600-55341400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:55340600-55341400	Enhancers	Adipose Nuclei	Adipose
46	chr2:55340600-55342600	Weak transcription	HUVEC	blood vessel
47	chr2:55340600-55344400	Weak transcription	Brain Germinal Matrix	brain
48	chr2:55340600-55345200	Weak transcription	Fetal Brain Male	brain
49	chr2:55340600-55347000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:55340800-55341800	Enhancers	Brain Inferior Temporal Lobe	brain

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