Variant report

Variant	rs3782323
Chromosome Location	chr12:50482921-50482922
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50482709..50484515-chr12:50550134..50551963,2	K562	blood:
2	chr12:50475132..50479699-chr12:50479828..50484275,5	K562	blood:
3	chr12:50478595..50483647-chr12:50502911..50507517,7	K562	blood:
4	chr12:50482227..50482988-chr12:50505180..50505752,2	MCF-7	breast:
5	chr12:50482430..50484025-chr12:50560178..50562412,2	K562	blood:
6	chr12:50478759..50480659-chr12:50481009..50483998,3	K562	blood:
7	chr12:50360514..50361388-chr12:50482297..50482976,2	K562	blood:
8	chr12:50481586..50483446-chr12:50561055..50562611,2	MCF-7	breast:
9	chr12:50475972..50484033-chr12:50500850..50507517,14	K562	blood:
10	chr12:50482709..50485025-chr12:50550134..50552131,3	K562	blood:
11	chr12:50477567..50484756-chr12:50559008..50565131,16	MCF-7	breast:
12	chr12:50468886..50470594-chr12:50481318..50483189,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000110881	Chromatin interaction
ENSG00000139624	Chromatin interaction
ENSG00000272368	Chromatin interaction
ENSG00000086159	Chromatin interaction
ENSG00000066117	Chromatin interaction
ENSG00000178449	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10783336	0.81[GIH][hapmap]
rs10783337	0.81[GIH][hapmap]
rs10783341	0.83[CHB][hapmap]
rs10875997	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10876006	0.81[GIH][hapmap]
rs10876007	0.83[CHB][hapmap]
rs17124448	0.92[GIH][hapmap]
rs2242507	0.92[GIH][hapmap]
rs2272391	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs2277355	0.89[GIH][hapmap]
rs7139363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7305558	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3782323	MCRS1	cis	parietal	SCAN
rs3782323	RND1	cis	parietal	SCAN
rs3782323	GRASP	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50479800-50488200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:50480000-50483600	Weak transcription	Right Ventricle	heart
3	chr12:50480000-50485400	Weak transcription	Stomach Mucosa	stomach
4	chr12:50480000-50486000	Strong transcription	Colon Smooth Muscle	Colon
5	chr12:50480000-50494800	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr12:50480000-50496400	Weak transcription	Right Atrium	heart
7	chr12:50480200-50483000	Genic enhancers	HepG2	liver
8	chr12:50480200-50483000	Genic enhancers	NH-A	brain
9	chr12:50480200-50484200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:50480200-50484800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:50480200-50489400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:50480200-50494800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:50480200-50494800	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:50480200-50496200	Strong transcription	Fetal Muscle Trunk	muscle
15	chr12:50480200-50496600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr12:50480200-50496600	Strong transcription	Thymus	Thymus
17	chr12:50480200-50496800	Strong transcription	Fetal Stomach	stomach
18	chr12:50480400-50483200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
19	chr12:50480400-50486400	Strong transcription	K562	blood
20	chr12:50480400-50493800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:50480400-50494400	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr12:50480400-50494400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:50480400-50494600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr12:50480400-50494800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:50480400-50494800	Strong transcription	Duodenum Mucosa	Duodenum
26	chr12:50480400-50494800	Strong transcription	Fetal Intestine Large	intestine
27	chr12:50480400-50494800	Strong transcription	Placenta	Placenta
28	chr12:50480400-50495600	Strong transcription	Stomach Smooth Muscle	stomach
29	chr12:50480400-50495800	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr12:50480400-50496000	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr12:50480400-50496200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr12:50480400-50496200	Strong transcription	A549	lung
33	chr12:50480400-50496600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:50480400-50496600	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr12:50480400-50496600	Strong transcription	Primary T cells from cord blood	blood
36	chr12:50480400-50496600	Strong transcription	Fetal Lung	lung
37	chr12:50480600-50483000	Genic enhancers	Brain Inferior Temporal Lobe	brain
38	chr12:50480600-50483200	Genic enhancers	NHDF-Ad	bronchial
39	chr12:50480600-50483400	Genic enhancers	Muscle Satellite Cultured Cells	--
40	chr12:50480600-50486000	Strong transcription	Rectal Smooth Muscle	rectum
41	chr12:50480600-50491000	Strong transcription	Hela-S3	cervix
42	chr12:50480600-50492200	Strong transcription	Primary hematopoietic stem cells	blood
43	chr12:50480600-50493200	Strong transcription	Adipose Nuclei	Adipose
44	chr12:50480600-50493600	Strong transcription	HSMMtube	muscle
45	chr12:50480600-50494000	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr12:50480600-50494600	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr12:50480600-50494600	Strong transcription	Left Ventricle	heart
48	chr12:50480600-50494800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr12:50480600-50494800	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr12:50480600-50495000	Strong transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links