Variant report

Variant	rs1948425
Chromosome Location	chr12:46778881-46778882
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46657863..46660351-chr12:46778251..46780364,2	MCF-7	breast:
2	chr12:46495435..46496952-chr12:46778066..46780745,2	MCF-7	breast:
3	chr12:46776676..46779494-chr12:106750626..106752443,2	MCF-7	breast:
4	chr12:46778629..46780721-chr12:46796448..46799296,3	K562	blood:
5	chr12:46778280..46780427-chr12:46916200..46918090,2	MCF-7	breast:
6	chr12:46778324..46780021-chr12:46941195..46943535,2	K562	blood:
7	chr12:46778278..46780739-chr12:46799465..46801687,2	K562	blood:
8	chr12:46660942..46665525-chr12:46775819..46780739,12	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000111371	Chromatin interaction
ENSG00000013503	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11183453	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183454	0.94[JPT][hapmap]
rs1125908	0.94[JPT][hapmap]
rs11833812	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11834593	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17096884	0.89[JPT][hapmap]
rs2125646	0.84[JPT][hapmap]
rs2307059	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2307062	0.84[JPT][hapmap]
rs2307063	0.84[JPT][hapmap]
rs2408509	0.84[JPT][hapmap]
rs3742061	0.89[JPT][hapmap]
rs55795804	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57199226	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57786829	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58545634	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59546893	0.96[EUR][1000 genomes]
rs73282593	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967840	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46776600-46779600	Active TSS	H9 Cell Line	embryonic stem cell
2	chr12:46776800-46779000	Active TSS	GM12878-XiMat	blood
3	chr12:46776800-46779200	Active TSS	H1 Cell Line	embryonic stem cell
4	chr12:46776800-46779200	Active TSS	K562	blood
5	chr12:46777600-46779000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr12:46777600-46779600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:46777800-46779400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr12:46777800-46779600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:46777800-46779600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr12:46777800-46779800	Flanking Active TSS	Hela-S3	cervix
11	chr12:46778000-46779000	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr12:46778000-46779200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:46778000-46779200	Weak transcription	Spleen	Spleen
14	chr12:46778000-46779600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:46778000-46779600	Flanking Active TSS	Liver	Liver
16	chr12:46778000-46781200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr12:46778200-46779200	Weak transcription	Lung	lung
18	chr12:46778200-46779600	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr12:46778200-46779600	Flanking Active TSS	A549	lung
20	chr12:46778200-46779600	Flanking Active TSS	NHEK	skin
21	chr12:46778200-46784800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:46778400-46779000	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr12:46778400-46779200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr12:46778400-46779200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:46778400-46779200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:46778400-46779200	Weak transcription	Aorta	Aorta
27	chr12:46778400-46779200	Weak transcription	Brain Substantia Nigra	brain
28	chr12:46778400-46779200	Weak transcription	Esophagus	oesophagus
29	chr12:46778400-46779200	Weak transcription	Gastric	stomach
30	chr12:46778400-46779200	Weak transcription	Ovary	ovary
31	chr12:46778400-46779200	Weak transcription	Pancreas	Pancrea
32	chr12:46778400-46779200	Weak transcription	Psoas Muscle	Psoas
33	chr12:46778400-46779200	Weak transcription	Right Ventricle	heart
34	chr12:46778400-46779200	Weak transcription	Stomach Mucosa	stomach
35	chr12:46778400-46779200	Enhancers	Osteobl	bone
36	chr12:46778400-46779600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr12:46778400-46779600	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr12:46778400-46779600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:46778400-46779600	Enhancers	Placenta	Placenta
40	chr12:46778400-46779600	Enhancers	Small Intestine	intestine
41	chr12:46778400-46780200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr12:46778400-46780200	Weak transcription	Fetal Brain Male	brain
43	chr12:46778400-46780400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr12:46778400-46780600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr12:46778400-46780600	Enhancers	HSMMtube	muscle
46	chr12:46778400-46780800	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr12:46778400-46780800	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr12:46778400-46780800	Weak transcription	Fetal Muscle Trunk	muscle
49	chr12:46778400-46781000	Enhancers	Primary B cells from peripheral blood	blood
50	chr12:46778400-46781400	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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