Variant report

Variant	rs3741560
Chromosome Location	chr12:50366754-50366755
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50316423..50318171-chr12:50364926..50367311,2	K562	blood:

Variant related genes	Relation type
ENSG00000257771	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12306363	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17124205	0.92[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17124219	0.83[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17124220	0.84[ASW][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59481807	0.91[AMR][1000 genomes];0.89[EUR][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:33 , 50 per page) page: 1

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	chr12:50361800-50367800	Enhancers	Brain Hippocampus Middle	brain
4	chr12:50362000-50367000	Enhancers	Brain Anterior Caudate	brain
5	chr12:50362000-50371200	Weak transcription	Fetal Brain Female	brain
6	chr12:50362400-50367400	Weak transcription	Brain Germinal Matrix	brain
7	chr12:50362600-50385800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:50363200-50368200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:50364000-50368600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr12:50364200-50367200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:50364200-50371000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:50364800-50367400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr12:50365200-50367400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:50365800-50367800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:50365800-50368200	Weak transcription	Fetal Brain Male	brain
16	chr12:50365800-50369200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:50366000-50367800	Weak transcription	Brain Angular Gyrus	brain
18	chr12:50366200-50366800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:50366200-50367000	Flanking Bivalent TSS/Enh	HepG2	liver
20	chr12:50366200-50368000	Weak transcription	Ovary	ovary
21	chr12:50366200-50368200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:50366200-50369800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr12:50366400-50366800	Bivalent Enhancer	Fetal Intestine Large	intestine
24	chr12:50366400-50367000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:50366400-50367400	Enhancers	Gastric	stomach
26	chr12:50366400-50367800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr12:50366400-50374600	Weak transcription	Fetal Kidney	kidney
28	chr12:50366600-50366800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:50366600-50368200	Enhancers	Brain Substantia Nigra	brain
30	chr12:50366600-50368200	Weak transcription	Right Ventricle	heart
31	chr12:50366600-50368400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:50366600-50368800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:50366600-50377400	Weak transcription	NHEK	skin

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