Variant report

Variant	rs59250711
Chromosome Location	chr12:49921889-49921890
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49921712..49923511-chr12:49960745..49963724,3	MCF-7	breast:
2	chr12:49921630..49924042-chr12:49926070..49928576,2	K562	blood:
3	chr12:49920492..49922115-chr12:49926233..49928971,2	MCF-7	breast:
4	chr12:49743272..49745246-chr12:49919993..49922237,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178401	Chromatin interaction
ENSG00000187778	Chromatin interaction
ENSG00000110844	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11169055	1.00[AMR][1000 genomes]
rs11830622	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11834883	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11836969	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12296998	1.00[AMR][1000 genomes]
rs12298123	1.00[AMR][1000 genomes]
rs12298506	1.00[AMR][1000 genomes]
rs12300085	1.00[AMR][1000 genomes]
rs12306942	1.00[AMR][1000 genomes]
rs12309399	1.00[AMR][1000 genomes]
rs12310046	1.00[AMR][1000 genomes]
rs12311319	1.00[AMR][1000 genomes]
rs12311910	1.00[AMR][1000 genomes]
rs12313583	1.00[AMR][1000 genomes]
rs12314348	1.00[AMR][1000 genomes]
rs12315746	1.00[AMR][1000 genomes]
rs12315941	1.00[AMR][1000 genomes]
rs12318913	1.00[AMR][1000 genomes]
rs12320104	1.00[AMR][1000 genomes]
rs12320434	1.00[AMR][1000 genomes]
rs12320612	1.00[AMR][1000 genomes]
rs12321717	1.00[AMR][1000 genomes]
rs13377828	1.00[AMR][1000 genomes]
rs57970210	1.00[AMR][1000 genomes]
rs58867453	1.00[AMR][1000 genomes]
rs59570650	1.00[AMR][1000 genomes]
rs60254449	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60507124	1.00[AMR][1000 genomes]
rs60658484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61122194	0.86[AFR][1000 genomes]
rs61227990	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv899069	chr12:49760499-49924637	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv899070	chr12:49811311-49941500	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv518746	chr12:49870964-49924637	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	esv1801776	chr12:49915354-49934565	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49888800-49927800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:49905200-49927000	Weak transcription	Fetal Heart	heart
3	chr12:49909600-49925600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr12:49911000-49923000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:49911200-49922000	Strong transcription	Fetal Intestine Large	intestine
6	chr12:49912600-49926400	Strong transcription	Fetal Muscle Trunk	muscle
7	chr12:49912800-49922600	Strong transcription	Fetal Muscle Leg	muscle
8	chr12:49913200-49922400	Strong transcription	A549	lung
9	chr12:49913200-49923600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:49913800-49922000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr12:49914000-49922600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:49914400-49931400	Weak transcription	Pancreas	Pancrea
13	chr12:49914800-49922000	Strong transcription	Muscle Satellite Cultured Cells	--
14	chr12:49915000-49922600	Strong transcription	GM12878-XiMat	blood
15	chr12:49915000-49925600	Weak transcription	Small Intestine	intestine
16	chr12:49915400-49922000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:49916200-49922200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:49916400-49922400	Strong transcription	Fetal Stomach	stomach
19	chr12:49916400-49931200	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr12:49916600-49922000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr12:49916800-49923000	Strong transcription	Fetal Intestine Small	intestine
22	chr12:49916800-49927200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr12:49917600-49931200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr12:49917800-49922000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr12:49918000-49922000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr12:49918000-49922000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:49918000-49922000	Strong transcription	Dnd41	blood
28	chr12:49918000-49922000	Strong transcription	NH-A	brain
29	chr12:49918000-49922400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:49918200-49922000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:49918200-49922000	Strong transcription	NHLF	lung
32	chr12:49918200-49922400	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr12:49918200-49922800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:49918200-49922800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr12:49918400-49922000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:49918400-49922000	Strong transcription	Adipose Nuclei	Adipose
37	chr12:49918400-49922000	Strong transcription	Lung	lung
38	chr12:49918400-49922000	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr12:49918400-49922000	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr12:49918400-49922000	Strong transcription	Hela-S3	cervix
41	chr12:49918400-49922000	Strong transcription	HSMM	muscle
42	chr12:49918400-49922000	Strong transcription	HSMMtube	muscle
43	chr12:49918400-49922000	Strong transcription	NHEK	skin
44	chr12:49918400-49922400	Strong transcription	Fetal Lung	lung
45	chr12:49918800-49923600	Strong transcription	HUVEC	blood vessel
46	chr12:49919000-49922000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:49919000-49922000	Strong transcription	Osteobl	bone
48	chr12:49919200-49923200	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr12:49919200-49924600	Weak transcription	Brain Angular Gyrus	brain
50	chr12:49919200-49925400	Weak transcription	Liver	Liver

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