Variant report

Variant	rs296748
Chromosome Location	chr12:50368013-50368014
allele	C/T
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50260625..50261504-chr12:50367677..50368552,3	MCF-7	breast:
2	chr12:50367636..50371210-chr12:50373031..50375237,3	K562	blood:
3	chr12:50015023..50017139-chr12:50367561..50369518,2	K562	blood:
4	chr12:50258974..50260618-chr12:50366779..50369622,2	MCF-7	breast:
5	chr12:50367709..50369586-chr12:50462445..50464458,2	MCF-7	breast:
6	chr12:50367042..50370413-chr12:50441830..50446012,4	K562	blood:
7	chr12:50366961..50368712-chr12:50409103..50412073,2	K562	blood:
8	chr12:50367721..50368617-chr12:50449659..50451716,5	MCF-7	breast:
9	chr12:50367696..50368951-chr12:50463985..50464557,3	MCF-7	breast:
10	chr12:50367707..50368705-chr12:50449431..50450774,7	MCF-7	breast:
11	chr12:50367744..50368598-chr12:50463753..50464919,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000110881	Chromatin interaction
ENSG00000161800	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11169179	1.00[EUR][1000 genomes]
rs11169181	1.00[EUR][1000 genomes]
rs11169252	0.80[ASN][1000 genomes]
rs12313336	0.87[ASN][1000 genomes]
rs12313701	0.87[ASN][1000 genomes]
rs12316969	1.00[EUR][1000 genomes]
rs12318294	1.00[EUR][1000 genomes]
rs2697111	1.00[EUR][1000 genomes]
rs296738	1.00[EUR][1000 genomes]
rs296749	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs296753	1.00[EUR][1000 genomes]
rs296755	1.00[EUR][1000 genomes]
rs296757	1.00[EUR][1000 genomes]
rs296758	1.00[EUR][1000 genomes]
rs296761	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs296764	1.00[EUR][1000 genomes]
rs296765	1.00[EUR][1000 genomes]
rs372753	1.00[EUR][1000 genomes]
rs425726	1.00[EUR][1000 genomes]
rs455037	1.00[EUR][1000 genomes]
rs58424082	0.87[ASN][1000 genomes]
rs60009415	1.00[EUR][1000 genomes]
rs61147017	0.87[ASN][1000 genomes]
rs672697	1.00[EUR][1000 genomes]
rs73297484	0.87[ASN][1000 genomes]
rs73297487	0.87[ASN][1000 genomes]
rs73297491	0.87[ASN][1000 genomes]
rs73310966	1.00[EUR][1000 genomes]
rs74087196	1.00[EUR][1000 genomes]
rs7972448	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv832407	chr12:50243268-50412236	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv558835	chr12:50275137-50433234	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv899072	chr12:50326176-50379667	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	esv1827130	chr12:50349765-50379667	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv469374	chr12:50349765-50467769	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv469375	chr12:50349765-50467769	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv558837	chr12:50349765-50467769	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50361400-50372800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:50361600-50368200	Weak transcription	Right Atrium	heart
3	chr12:50362000-50371200	Weak transcription	Fetal Brain Female	brain
4	chr12:50362600-50385800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:50363200-50368200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:50364000-50368600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:50364200-50371000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:50365800-50368200	Weak transcription	Fetal Brain Male	brain
9	chr12:50365800-50369200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:50366200-50368200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:50366200-50369800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr12:50366400-50374600	Weak transcription	Fetal Kidney	kidney
13	chr12:50366600-50368200	Enhancers	Brain Substantia Nigra	brain
14	chr12:50366600-50368200	Weak transcription	Right Ventricle	heart
15	chr12:50366600-50368400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:50366600-50368800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:50366600-50377400	Weak transcription	NHEK	skin
18	chr12:50366800-50368200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:50366800-50369200	Enhancers	Liver	Liver
20	chr12:50367000-50368200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr12:50367000-50369600	Enhancers	Fetal Intestine Large	intestine
22	chr12:50367000-50369800	Enhancers	Fetal Intestine Small	intestine
23	chr12:50367000-50378000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:50367200-50369200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:50367400-50368200	Enhancers	Brain Cingulate Gyrus	brain
26	chr12:50367400-50369000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:50367400-50369000	Flanking Bivalent TSS/Enh	HepG2	liver
28	chr12:50367400-50401200	Weak transcription	Gastric	stomach
29	chr12:50367600-50368400	Enhancers	Colonic Mucosa	Colon
30	chr12:50367600-50369200	Enhancers	Duodenum Mucosa	Duodenum
31	chr12:50367600-50374800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:50367800-50368200	Enhancers	Brain Angular Gyrus	brain
33	chr12:50367800-50368200	Enhancers	Brain Anterior Caudate	brain
34	chr12:50367800-50368200	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr12:50367800-50368200	Enhancers	Colon Smooth Muscle	Colon
36	chr12:50367800-50368200	Bivalent Enhancer	Fetal Stomach	stomach
37	chr12:50367800-50368400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:50367800-50368400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr12:50367800-50368400	Enhancers	Left Ventricle	heart
40	chr12:50367800-50368400	Enhancers	Pancreas	Pancrea
41	chr12:50367800-50368600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:50367800-50368600	Enhancers	Stomach Mucosa	stomach
43	chr12:50367800-50368800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
44	chr12:50367800-50369200	Enhancers	Rectal Smooth Muscle	rectum
45	chr12:50367800-50369200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
46	chr12:50367800-50370000	Enhancers	Fetal Heart	heart
47	chr12:50367800-50370800	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr12:50368000-50368200	Enhancers	Brain Hippocampus Middle	brain
49	chr12:50368000-50368200	Enhancers	Stomach Smooth Muscle	stomach
50	chr12:50368000-50368600	Enhancers	Monocytes-CD14+_RO01746	blood

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