Variant report

Variant	rs17541307
Chromosome Location	chr2:47272903-47272904
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47271650..47273427-chr2:47295265..47298001,2	MCF-7	breast:
2	chr2:47266042..47270456-chr2:47271373..47275642,6	K562	blood:
3	chr2:47179225..47182053-chr2:47271566..47273267,2	K562	blood:

Variant related genes	Relation type
ENSG00000233845	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10495942	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11884118	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11890603	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11901122	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13353361	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13423726	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17036138	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17481182	1.00[ASW][hapmap]
rs17541155	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3814037	0.81[AMR][1000 genomes]
rs55654462	0.91[AMR][1000 genomes]
rs56139747	0.91[AMR][1000 genomes]
rs56200787	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73929358	0.84[AMR][1000 genomes]
rs7581528	0.84[GIH][hapmap]

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	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
9	nsv984437	chr2:47270533-47307361	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 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	chr2:47263000-47283200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:47263400-47283200	Weak transcription	Fetal Kidney	kidney
16	chr2:47265000-47273200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:47265000-47273400	Weak transcription	K562	blood
18	chr2:47266200-47280800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr2:47266400-47280200	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr2:47266400-47283000	Strong transcription	Primary T cells from cord blood	blood
21	chr2:47266600-47282600	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr2:47266800-47282800	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr2:47267200-47281400	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr2:47267200-47282800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr2:47267400-47273200	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr2:47267400-47282600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:47268200-47273000	Enhancers	Brain Anterior Caudate	brain
28	chr2:47268600-47273000	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr2:47268600-47274000	Enhancers	Brain Cingulate Gyrus	brain
30	chr2:47268600-47282000	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr2:47270000-47282800	Strong transcription	Primary hematopoietic stem cells	blood
32	chr2:47270000-47282800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:47270200-47280200	Strong transcription	GM12878-XiMat	blood
34	chr2:47270400-47282200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:47270400-47282400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:47270400-47282800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:47270600-47273200	Strong transcription	Duodenum Mucosa	Duodenum
38	chr2:47270600-47275800	Strong transcription	Fetal Intestine Large	intestine
39	chr2:47270600-47278800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr2:47270800-47273200	Enhancers	Brain Angular Gyrus	brain
41	chr2:47270800-47279000	Weak transcription	Fetal Lung	lung
42	chr2:47270800-47296600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr2:47271000-47273000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:47271000-47273000	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:47271000-47273000	Weak transcription	Pancreas	Pancrea
46	chr2:47271000-47277200	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:47271000-47277600	Weak transcription	Stomach Mucosa	stomach
48	chr2:47271200-47273000	Strong transcription	Lung	lung
49	chr2:47271200-47273200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:47271200-47273600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links