Variant report

Variant	rs56260598
Chromosome Location	chr12:123361993-123361994
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123359999..123363082-chr12:123363364..123366412,4	MCF-7	breast:
2	chr12:123361905..123363893-chr12:123371746..123374359,2	MCF-7	breast:
3	chr12:123358138..123360225-chr12:123360853..123363329,2	MCF-7	breast:
4	chr12:123336928..123338440-chr12:123360381..123363029,2	K562	blood:

Variant related genes	Relation type
ENSG00000130787	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1619142	0.80[EUR][1000 genomes]
rs1671681	0.80[EUR][1000 genomes]
rs1671682	0.80[EUR][1000 genomes]
rs1671683	0.80[EUR][1000 genomes]
rs1696316	0.80[EUR][1000 genomes]
rs1696322	0.80[EUR][1000 genomes]
rs1696325	0.80[EUR][1000 genomes]
rs1798560	0.80[EUR][1000 genomes]
rs1798561	0.80[EUR][1000 genomes]
rs1798565	0.80[EUR][1000 genomes]
rs1798569	0.80[EUR][1000 genomes]
rs2456151	0.80[EUR][1000 genomes]
rs2649899	0.80[EUR][1000 genomes]
rs55650312	0.92[EUR][1000 genomes]
rs55716280	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56294931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59058900	0.84[EUR][1000 genomes]
rs59769449	0.84[EUR][1000 genomes]
rs73415582	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123355800-123363600	Weak transcription	Dnd41	blood
2	chr12:123356200-123368600	Weak transcription	Hela-S3	cervix
3	chr12:123356400-123362400	Enhancers	Liver	Liver
4	chr12:123356600-123364200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:123356800-123362200	Enhancers	Primary T cells fromperipheralblood	blood
6	chr12:123356800-123363600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:123356800-123369200	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr12:123356800-123370000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr12:123357000-123362400	Enhancers	Brain Hippocampus Middle	brain
10	chr12:123357000-123362800	Enhancers	Fetal Muscle Trunk	muscle
11	chr12:123357000-123365600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:123357000-123369800	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr12:123357000-123373000	Weak transcription	Aorta	Aorta
14	chr12:123357200-123362000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr12:123357200-123362200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:123357200-123362400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:123357200-123363800	Weak transcription	K562	blood
18	chr12:123357200-123365200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:123357800-123362800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:123358200-123367200	Weak transcription	HUVEC	blood vessel
21	chr12:123358600-123363400	Weak transcription	Esophagus	oesophagus
22	chr12:123358800-123362000	Weak transcription	Fetal Stomach	stomach
23	chr12:123358800-123371400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr12:123359000-123362000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr12:123359000-123365000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:123359000-123365200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:123359000-123368400	Weak transcription	Fetal Intestine Large	intestine
28	chr12:123359000-123369600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr12:123359400-123366000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr12:123359600-123362200	Enhancers	Fetal Muscle Leg	muscle
31	chr12:123359600-123365000	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr12:123359600-123366200	Enhancers	Right Atrium	heart
33	chr12:123359800-123362200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:123359800-123362400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:123360000-123362000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:123360000-123362400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:123360000-123362400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:123360000-123362400	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr12:123360000-123362600	Enhancers	Adipose Nuclei	Adipose
40	chr12:123360200-123362000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:123360200-123362000	Enhancers	HSMMtube	muscle
42	chr12:123360200-123362000	Enhancers	NH-A	brain
43	chr12:123360200-123362000	Enhancers	NHLF	lung
44	chr12:123360200-123362400	Genic enhancers	NHEK	skin
45	chr12:123360200-123362600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:123360200-123363600	Strong transcription	Fetal Intestine Small	intestine
47	chr12:123360400-123362400	Enhancers	GM12878-XiMat	blood
48	chr12:123360400-123363600	Weak transcription	Gastric	stomach
49	chr12:123360400-123363800	Weak transcription	Colonic Mucosa	Colon
50	chr12:123360400-123365400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links