Variant report

Variant	rs1055417
Chromosome Location	chr1:171483717-171483718
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171482500..171484395-chr1:171486369..171488857,2	K562	blood:
2	chr1:171480931..171484938-chr1:171487047..171489440,3	MCF-7	breast:
3	chr1:171476248..171479748-chr1:171482542..171484607,3	MCF-7	breast:
4	chr1:171455198..171457522-chr1:171482757..171484309,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117523	Chromatin interaction
ENSG00000201126	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10913167	1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12119596	0.90[ASN][1000 genomes]
rs12129856	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131694	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12136576	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12137832	1.00[CHB][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12139715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12142594	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12145045	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12145085	0.85[EUR][1000 genomes]
rs12146022	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12733939	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12734261	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12759907	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171005	0.85[EUR][1000 genomes]
rs183533	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs190198	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2294292	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235471	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235472	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235477	0.82[EUR][1000 genomes]
rs235488	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs235495	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs235498	0.88[EUR][1000 genomes]
rs235502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs235507	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs235886	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs235892	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs235893	0.85[EUR][1000 genomes]
rs235895	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs235897	0.85[EUR][1000 genomes]
rs235898	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs235899	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs235900	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs235901	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs235902	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs235903	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs235904	0.82[EUR][1000 genomes]
rs235910	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs235911	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs235912	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs46407	0.81[EUR][1000 genomes]
rs56207586	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs591286	0.85[EUR][1000 genomes]
rs67133611	0.82[EUR][1000 genomes]
rs71637410	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71637418	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71637419	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74122850	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534464	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7534557	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.89[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7538745	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][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	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv465639	chr1:171459507-171545051	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv548190	chr1:171459507-171545051	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1055417	SELE	cis	cerebellum	SCAN
rs1055417	MYOC	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171470600-171491600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:171471400-171485800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:171472000-171483800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:171472600-171483800	Weak transcription	Fetal Stomach	stomach
5	chr1:171473200-171486400	Weak transcription	Pancreas	Pancrea
6	chr1:171475400-171484000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:171475400-171486200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:171475800-171484400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:171475800-171486400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:171475800-171524400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:171476000-171498800	Weak transcription	Fetal Heart	heart
12	chr1:171476200-171486600	Weak transcription	Brain Substantia Nigra	brain
13	chr1:171476400-171483800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:171476600-171489000	Weak transcription	Right Ventricle	heart
15	chr1:171477400-171484000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:171477400-171486600	Weak transcription	Brain Angular Gyrus	brain
17	chr1:171477600-171486400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:171478400-171485800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:171478800-171483800	Weak transcription	A549	lung
20	chr1:171478800-171497800	Weak transcription	Stomach Mucosa	stomach
21	chr1:171479000-171485800	Weak transcription	Small Intestine	intestine
22	chr1:171480000-171485800	Weak transcription	Ovary	ovary
23	chr1:171480200-171484200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:171480600-171486400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:171481000-171528000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:171481200-171492800	Strong transcription	Primary B cells from cord blood	blood
27	chr1:171481200-171495600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:171481200-171518800	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:171481200-171519200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:171481200-171519600	Strong transcription	Dnd41	blood
31	chr1:171481200-171520000	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr1:171481200-171522400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:171481400-171489000	Strong transcription	HSMM	muscle
34	chr1:171481400-171519200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:171481400-171519800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr1:171481400-171520000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:171481400-171522800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:171481600-171487200	Strong transcription	NHEK	skin
39	chr1:171481600-171494600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:171481600-171519200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:171481600-171520600	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr1:171481800-171483800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr1:171481800-171495000	Strong transcription	HUVEC	blood vessel
44	chr1:171481800-171520000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:171481800-171520600	Strong transcription	Placenta	Placenta
46	chr1:171482000-171483800	Strong transcription	GM12878-XiMat	blood
47	chr1:171482000-171495600	Strong transcription	HMEC	breast
48	chr1:171482000-171519800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr1:171482000-171520000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr1:171482000-171520400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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