Variant report

Variant	rs1212352
Chromosome Location	chr1:154239283-154239284
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154192034..154195055-chr1:154237858..154241372,4	MCF-7	breast:
2	chr1:154236442..154241812-chr1:154243586..154247600,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143569	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000143575	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1044013	0.81[EUR][1000 genomes]
rs10797067	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11265122	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs11265299	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1194593	0.82[EUR][1000 genomes]
rs1194596	0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs12026475	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap]
rs12405309	0.86[JPT][hapmap]
rs12408458	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1760800	0.84[EUR][1000 genomes]
rs3828076	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4521985	0.82[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs4845363	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs4845597	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs4845600	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs4845601	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs6659053	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs6664278	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs6667928	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs6671166	0.86[JPT][hapmap]
rs6678826	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs7535778	0.82[JPT][hapmap]
rs7551128	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1212352	C1orf43	cis	parietal	SCAN
rs1212352	SPRR2D	cis	parietal	SCAN
rs1212352	LASS2	cis	parietal	SCAN
rs1212352	GOLPH3L	cis	cerebellum	SCAN
rs1212352	UBAP2L	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154195600-154244000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:154196200-154243800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:154196400-154243800	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:154196600-154243600	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:154196800-154242600	Strong transcription	A549	lung
6	chr1:154197000-154242800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:154197000-154243200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:154197000-154243600	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:154197000-154243800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:154197000-154243800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:154197200-154243600	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:154197200-154244000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:154197400-154242800	Strong transcription	Brain Anterior Caudate	brain
14	chr1:154197600-154239400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:154197600-154239800	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr1:154197600-154239800	Strong transcription	NHLF	lung
17	chr1:154197600-154242000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:154197600-154243000	Strong transcription	Primary B cells from peripheral blood	blood
19	chr1:154197600-154243600	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr1:154197600-154243600	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr1:154197600-154243600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:154197600-154243600	Strong transcription	Thymus	Thymus
23	chr1:154197600-154243800	Strong transcription	Adipose Nuclei	Adipose
24	chr1:154197600-154244000	Strong transcription	Fetal Muscle Leg	muscle
25	chr1:154197800-154239600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:154197800-154242000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:154197800-154243600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:154197800-154243600	Strong transcription	Placenta	Placenta
29	chr1:154197800-154243800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:154198000-154243000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:154198000-154243800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr1:154198200-154241000	Strong transcription	Dnd41	blood
33	chr1:154198400-154243000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:154199000-154243600	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:154199400-154243600	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:154200000-154243800	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr1:154211000-154243800	Strong transcription	Fetal Intestine Large	intestine
38	chr1:154212000-154239600	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:154212200-154239800	Strong transcription	Liver	Liver
40	chr1:154212800-154240200	Strong transcription	Left Ventricle	heart
41	chr1:154213000-154242800	Strong transcription	Colon Smooth Muscle	Colon
42	chr1:154213600-154243800	Strong transcription	Brain Hippocampus Middle	brain
43	chr1:154214000-154239600	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr1:154214000-154239600	Strong transcription	HMEC	breast
45	chr1:154214000-154243600	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr1:154214000-154243800	Strong transcription	Stomach Smooth Muscle	stomach
47	chr1:154214200-154242800	Strong transcription	NHEK	skin
48	chr1:154219800-154244600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr1:154220000-154243200	Strong transcription	Lung	lung
50	chr1:154221200-154239400	Strong transcription	HSMMtube	muscle

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