Variant report

Variant	rs3794215
Chromosome Location	chr12:121168083-121168084
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:121167755..121169709-chr12:121199569..121201088,2	K562	blood:
2	chr12:121166188..121170592-chr12:121174629..121177744,4	K562	blood:
3	chr12:121161440..121165409-chr12:121166157..121170080,9	K562	blood:
4	chr12:121160022..121162940-chr12:121166052..121168172,2	MCF-7	breast:
5	chr12:121166233..121168963-chr12:121173743..121176239,2	K562	blood:
6	chr12:121146305..121152610-chr12:121160959..121168394,8	MCF-7	breast:
7	chr12:121162994..121164820-chr12:121167005..121169099,2	MCF-7	breast:
8	chr12:121166701..121168249-chr12:121176996..121179213,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000175970	Chromatin interaction
ENSG00000256569	Chromatin interaction
ENSG00000265455	Chromatin interaction
ENSG00000122971	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11065223	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11065231	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11065233	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17847	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1814851	0.82[ASN][1000 genomes]
rs2393749	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34491494	0.85[AMR][1000 genomes]
rs3794214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3829290	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs3915	0.82[ASN][1000 genomes]
rs555404	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs575437	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs658521	0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs695952	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs696337	0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs696339	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs708783	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7308648	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7964786	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7976497	0.82[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7978125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899557	chr12:121069201-121189116	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh 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 miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv899558	chr12:121161589-121179939	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3794215	SPPL3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121164000-121177000	Weak transcription	Aorta	Aorta
2	chr12:121164200-121169800	Weak transcription	NH-A	brain
3	chr12:121164200-121170800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr12:121164200-121172600	Weak transcription	HSMMtube	muscle
5	chr12:121164200-121176400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:121164400-121168200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:121164400-121168200	Weak transcription	Gastric	stomach
8	chr12:121164400-121168200	Weak transcription	Osteobl	bone
9	chr12:121164400-121168400	Weak transcription	Fetal Brain Male	brain
10	chr12:121164400-121169000	Weak transcription	Brain Angular Gyrus	brain
11	chr12:121164400-121169800	Weak transcription	HSMM	muscle
12	chr12:121164400-121170400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:121164400-121170400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr12:121164400-121170600	Weak transcription	NHDF-Ad	bronchial
15	chr12:121164400-121170800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:121164400-121170800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:121164400-121174800	Weak transcription	Esophagus	oesophagus
18	chr12:121164400-121176000	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:121164400-121176600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:121164400-121177600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:121164400-121179600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr12:121164600-121168200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:121164600-121168200	Weak transcription	Colon Smooth Muscle	Colon
24	chr12:121164600-121168200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr12:121164600-121168600	Weak transcription	NHEK	skin
26	chr12:121164600-121169000	Strong transcription	Fetal Muscle Trunk	muscle
27	chr12:121164600-121172600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:121164600-121177000	Weak transcription	Small Intestine	intestine
29	chr12:121164600-121177200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr12:121164600-121178000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:121164800-121168200	Weak transcription	Brain Substantia Nigra	brain
32	chr12:121164800-121169000	Strong transcription	Thymus	Thymus
33	chr12:121164800-121169200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr12:121164800-121169400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:121164800-121169400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:121164800-121169400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:121164800-121169400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:121164800-121169400	Strong transcription	Fetal Stomach	stomach
39	chr12:121164800-121171600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr12:121164800-121173600	Weak transcription	GM12878-XiMat	blood
41	chr12:121164800-121178800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr12:121165000-121169000	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr12:121165000-121169000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:121165000-121169000	Strong transcription	Stomach Smooth Muscle	stomach
45	chr12:121165000-121169200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr12:121165000-121169200	Strong transcription	Fetal Muscle Leg	muscle
47	chr12:121165000-121169200	Strong transcription	Placenta	Placenta
48	chr12:121165000-121169200	Strong transcription	Left Ventricle	heart
49	chr12:121165000-121169400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:121165000-121175200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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