Variant report

Variant	rs3741502
Chromosome Location	chr12:56351937-56351938
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr12:56350829-56351996	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56223409..56227527-chr12:56348845..56352516,3	MCF-7	breast:
2	chr12:56210260..56213184-chr12:56348200..56352160,4	MCF-7	breast:
3	chr12:56350471..56352755-chr12:56510490..56512042,2	K562	blood:
4	chr12:56330972..56338064-chr12:56344899..56352450,13	MCF-7	breast:
5	chr12:56348195..56352007-chr12:56357444..56361194,9	MCF-7	breast:
6	chr12:56222034..56224424-chr12:56351051..56353709,2	MCF-7	breast:
7	chr12:56350213..56352992-chr12:56373952..56376823,2	MCF-7	breast:
8	chr12:56319350..56329795-chr12:56348492..56353182,19	MCF-7	breast:
9	chr12:56209766..56212313-chr12:56351329..56354004,2	MCF-7	breast:
10	chr12:56348719..56352915-chr12:56364675..56368847,8	MCF-7	breast:
11	chr12:56333047..56336022-chr12:56349677..56352067,3	K562	blood:
12	chr12:56324645..56327679-chr12:56350066..56352097,3	MCF-7	breast:
13	chr12:56350103..56352899-chr12:108954805..108957692,2	MCF-7	breast:
14	chr12:56351426..56355339-chr12:56358310..56361732,4	K562	blood:

No data

Variant related genes	Relation type
PMEL	TF binding region
ENSG00000111540	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000258554	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000237493	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000136003	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000075856	Chromatin interaction
ENSG00000182796	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1056784	1.00[YRI][hapmap]
rs12423802	1.00[YRI][hapmap]
rs12826115	1.00[YRI][hapmap]
rs17844787	1.00[YRI][hapmap]
rs2071024	1.00[YRI][hapmap]
rs2271191	1.00[YRI][hapmap]
rs3809134	1.00[ASW][hapmap]
rs7967075	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56328800-56352200	Weak transcription	Small Intestine	intestine
2	chr12:56345000-56352200	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr12:56345000-56353000	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr12:56345000-56353000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:56345000-56353600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:56345000-56354000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:56345400-56359000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:56345600-56353200	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr12:56346000-56352400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:56346400-56352400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr12:56346600-56360000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr12:56346800-56359400	Weak transcription	Brain Anterior Caudate	brain
13	chr12:56347000-56353800	Weak transcription	Ovary	ovary
14	chr12:56347000-56359600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:56347200-56360000	Weak transcription	HSMMtube	muscle
16	chr12:56347400-56352600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:56347400-56354200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:56347400-56359600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:56347400-56359800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:56347400-56359800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr12:56347600-56359800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr12:56347800-56359400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:56348000-56352400	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr12:56348200-56359400	Weak transcription	Liver	Liver
25	chr12:56348200-56359600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:56348200-56360000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:56348400-56359600	Weak transcription	Primary B cells from cord blood	blood
28	chr12:56348400-56359600	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr12:56348400-56359800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:56348400-56359800	Weak transcription	Fetal Lung	lung
31	chr12:56348800-56352200	Enhancers	Placenta	Placenta
32	chr12:56348800-56359600	Weak transcription	Spleen	Spleen
33	chr12:56349200-56352000	Enhancers	HMEC	breast
34	chr12:56349200-56355800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:56349200-56359600	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr12:56349200-56359600	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr12:56349400-56352000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:56349400-56352000	Enhancers	Esophagus	oesophagus
39	chr12:56349400-56354800	Weak transcription	Fetal Stomach	stomach
40	chr12:56349400-56359400	Weak transcription	Dnd41	blood
41	chr12:56349400-56359600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:56349400-56359600	Weak transcription	Thymus	Thymus
43	chr12:56349600-56352600	Enhancers	Fetal Intestine Large	intestine
44	chr12:56349600-56359400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr12:56349600-56359600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:56349800-56352200	Enhancers	Stomach Mucosa	stomach
47	chr12:56349800-56359600	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr12:56350000-56352000	Enhancers	NHEK	skin
49	chr12:56350000-56359800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:56350200-56353600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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