Variant report

Variant	rs28490098
Chromosome Location	chr2:47268939-47268940
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	CEBPB	chr2:47268824-47268941	K562	blood:	n/a	n/a
2	EP300	chr2:47267459-47271977	SK-N-SH	brain:	n/a	chr2:47271431-47271438

No.	Distal block	Cell Line	Cell type
1	chr2:47250659..47252384-chr2:47268724..47270646,2	MCF-7	breast:
2	chr2:47267673..47270387-chr2:47397211..47399730,2	K562	blood:
3	chr2:47266042..47270456-chr2:47271373..47275642,6	K562	blood:
4	chr2:47268939..47270470-chr2:47402039..47404588,3	MCF-7	breast:
5	chr2:47268893..47270456-chr2:47273694..47275642,2	K562	blood:

Variant related genes	Relation type
TTC7A	TF binding region
ENSG00000233845	TF binding region
ENSG00000068724	Chromatin interaction
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12373629	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13398062	1.00[ASN][1000 genomes]
rs55813111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55813407	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55829028	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55855730	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55920732	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6729896	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72808511	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72808512	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72808515	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72808516	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72808520	0.96[ASN][1000 genomes]
rs7563297	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv525197	chr2:47210747-47297973	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv984532	chr2:47237908-47270533	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv528091	chr2:47249239-47273732	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 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	chr2:47230200-47302800	Strong transcription	Dnd41	blood
2	chr2:47234400-47283600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:47236000-47278600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:47246000-47283800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr2:47246800-47281600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:47252000-47283400	Strong transcription	Thymus	Thymus
7	chr2:47255600-47273400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:47257000-47277000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:47258400-47282600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr2:47259600-47295000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:47261800-47273600	Weak transcription	Fetal Brain Female	brain
12	chr2:47262000-47283400	Weak transcription	Fetal Brain Male	brain
13	chr2:47262000-47283600	Weak transcription	Small Intestine	intestine
14	chr2:47262400-47269000	Weak transcription	Brain Germinal Matrix	brain
15	chr2:47262600-47269200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr2:47262800-47269000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:47262800-47269200	Genic enhancers	A549	lung
18	chr2:47262800-47269800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:47263000-47283200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:47263200-47269000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:47263200-47269200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:47263400-47270000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr2:47263400-47283200	Weak transcription	Fetal Kidney	kidney
24	chr2:47264600-47269000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:47265000-47273200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:47265000-47273400	Weak transcription	K562	blood
27	chr2:47265800-47269200	Weak transcription	Hela-S3	cervix
28	chr2:47266000-47269400	Genic enhancers	Placenta	Placenta
29	chr2:47266000-47270000	Enhancers	Colon Smooth Muscle	Colon
30	chr2:47266000-47270200	Enhancers	Brain Angular Gyrus	brain
31	chr2:47266000-47271600	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr2:47266200-47269200	Enhancers	Liver	Liver
33	chr2:47266200-47280800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr2:47266400-47269000	Weak transcription	HUVEC	blood vessel
35	chr2:47266400-47271000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:47266400-47280200	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr2:47266400-47283000	Strong transcription	Primary T cells from cord blood	blood
38	chr2:47266600-47269000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:47266600-47269000	Weak transcription	HMEC	breast
40	chr2:47266600-47269000	Weak transcription	NH-A	brain
41	chr2:47266600-47269600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr2:47266600-47272400	Enhancers	Brain Substantia Nigra	brain
43	chr2:47266600-47272800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:47266600-47282600	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr2:47266800-47269000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:47266800-47272600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:47266800-47282800	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr2:47267200-47269200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:47267200-47269400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:47267200-47269800	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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