Variant report

Variant	rs12275949
Chromosome Location	chr11:48061837-48061838
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	FOXA1	chr11:48061681-48062045	T-47D	breast:	n/a	n/a
2	FOXA1	chr11:48061732-48061987	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:48061733..48064075-chr11:48066877..48069020,2	K562	blood:
2	chr11:48060921..48063409-chr11:48064765..48066974,3	K562	blood:

Variant related genes	Relation type
PTPRJ	TF binding region
ENSG00000149177	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10466481	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11039501	1.00[EUR][1000 genomes]
rs11039502	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11039503	1.00[EUR][1000 genomes]
rs12278732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1228047	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1228048	0.93[AMR][1000 genomes]
rs1228050	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1228053	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12280964	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12281120	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12282774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12287023	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12290438	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60085783	1.00[EUR][1000 genomes]
rs6485803	1.00[EUR][1000 genomes]
rs7116563	1.00[EUR][1000 genomes]
rs7129454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1036451	chr11:47902321-48616646	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv541037	chr11:47902321-48616646	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1047490	chr11:47916708-48388686	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1044266	chr11:47929586-48276132	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv541038	chr11:47929586-48276132	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv1053145	chr11:47967902-48086950	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv870381	chr11:47989434-48142648	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
11	esv3396029	chr11:47993857-48241494	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
12	nsv897327	chr11:48004369-48911660	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	nsv869124	chr11:48014539-48783113	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv1051805	chr11:48016488-48378048	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
15	nsv428573	chr11:48032457-48152344	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
16	nsv897328	chr11:48043053-48901553	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
17	nsv897329	chr11:48052676-48319974	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:48047400-48073400	Weak transcription	HSMMtube	muscle
2	chr11:48047400-48073800	Weak transcription	Left Ventricle	heart
3	chr11:48050200-48068200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:48050800-48073000	Weak transcription	Esophagus	oesophagus
5	chr11:48051600-48071200	Weak transcription	Fetal Intestine Large	intestine
6	chr11:48051600-48073800	Weak transcription	Aorta	Aorta
7	chr11:48053600-48065400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr11:48053600-48065800	Weak transcription	Colonic Mucosa	Colon
9	chr11:48053800-48062600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr11:48053800-48065200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr11:48053800-48073400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr11:48054000-48062400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr11:48055200-48062400	Weak transcription	Lung	lung
14	chr11:48055600-48064800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr11:48055800-48063800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr11:48056800-48064000	Weak transcription	Stomach Mucosa	stomach
17	chr11:48056800-48064800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr11:48057000-48062600	Weak transcription	Liver	Liver
19	chr11:48057000-48062600	Weak transcription	Pancreas	Pancrea
20	chr11:48057000-48065200	Weak transcription	Colon Smooth Muscle	Colon
21	chr11:48057000-48065200	Weak transcription	Placenta	Placenta
22	chr11:48057000-48065400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr11:48057000-48065600	Weak transcription	Right Atrium	heart
24	chr11:48057000-48065600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr11:48057000-48066000	Weak transcription	Psoas Muscle	Psoas
26	chr11:48057000-48069800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr11:48057200-48062400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr11:48057600-48063600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr11:48057600-48064800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr11:48057800-48062400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr11:48057800-48062400	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr11:48058000-48062600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr11:48058000-48064200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr11:48058000-48064800	Weak transcription	Adipose Nuclei	Adipose
35	chr11:48058000-48064800	Weak transcription	Fetal Thymus	thymus
36	chr11:48058000-48068600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr11:48058000-48069600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr11:48058000-48073400	Weak transcription	K562	blood
39	chr11:48058200-48063600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr11:48058400-48063800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr11:48058400-48063800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr11:48058400-48063800	Weak transcription	NHLF	lung
43	chr11:48058400-48069600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr11:48058600-48062400	Weak transcription	Brain Angular Gyrus	brain
45	chr11:48058600-48063400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr11:48058600-48063400	Weak transcription	Osteobl	bone
47	chr11:48058600-48063800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr11:48058600-48064000	Weak transcription	Primary T cells from cord blood	blood
49	chr11:48058600-48064000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr11:48058600-48064200	Weak transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links