Variant report

Variant	rs715510
Chromosome Location	chr22:31690528-31690529
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:31685822..31687584-chr22:31689344..31691234,2	K562	blood:
2	chr22:31689960..31693778-chr22:31698735..31700616,3	MCF-7	breast:
3	chr22:31683915..31694680-chr22:31733392..31744713,34	MCF-7	breast:
4	chr22:31689966..31691795-chr22:31696089..31697952,2	K562	blood:
5	chr22:31684664..31691252-chr22:31735490..31744100,29	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100100	Chromatin interaction
ENSG00000213888	Chromatin interaction
ENSG00000100105	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1034588	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1034589	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs12152166	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13054220	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13056485	0.88[JPT][hapmap]
rs131205	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13158	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1858821	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2040533	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2073857	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2078803	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2079431	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2106294	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2228619	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2232170	0.85[CEU][hapmap]
rs2232176	0.85[CEU][hapmap]
rs2273249	0.95[CEU][hapmap]
rs2273251	0.95[CEU][hapmap]
rs2283879	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2283881	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2413033	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2413034	0.84[EUR][1000 genomes]
rs2413035	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2413046	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2413047	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2413049	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2899164	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs34545960	0.80[EUR][1000 genomes]
rs4141404	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4299418	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4603880	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820042	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4820043	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4820951	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4820955	1.00[CEU][hapmap]
rs4820962	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4820963	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749224	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs5749229	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5749243	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5749265	0.81[EUR][1000 genomes]
rs5749267	0.80[EUR][1000 genomes]
rs5749268	0.80[EUR][1000 genomes]
rs5749270	0.80[EUR][1000 genomes]
rs5753500	0.83[EUR][1000 genomes]
rs5753507	0.82[EUR][1000 genomes]
rs5753521	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753543	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5753597	0.81[EUR][1000 genomes]
rs5753601	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs5753609	0.90[CEU][hapmap]
rs5753610	0.80[EUR][1000 genomes]
rs5753632	0.95[CEU][hapmap]
rs5753639	0.95[CEU][hapmap]
rs5997902	0.85[EUR][1000 genomes]
rs5997912	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5997913	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs5997933	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5997939	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5997949	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71324184	0.87[EUR][1000 genomes]
rs714909	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7285619	0.95[CEU][hapmap]
rs7287267	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737684	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs737887	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737888	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs738657	0.95[CEU][hapmap]
rs8135344	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8135347	0.85[EUR][1000 genomes]
rs8138596	0.86[EUR][1000 genomes]
rs8141150	0.80[EUR][1000 genomes]
rs9606830	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606831	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606839	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs9606843	0.95[CEU][hapmap]
rs9609254	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609257	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9609264	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609265	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609266	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609267	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9609268	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9609277	0.80[EUR][1000 genomes]
rs9621235	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[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	nsv1067003	chr22:31558663-31697093	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1058844	chr22:31597104-31725296	Weak transcription Enhancers 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	23 gene(s)	inside rSNPs	diseases
3	nsv834176	chr22:31682426-31864701	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs715510	SFI1	cis	Thyroid	GTEx
rs715510	DRG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31688400-31693400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr22:31688600-31690600	Weak transcription	Small Intestine	intestine
3	chr22:31688600-31691200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr22:31688600-31691400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr22:31688600-31691800	Weak transcription	Left Ventricle	heart
6	chr22:31688800-31690800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr22:31688800-31691400	Weak transcription	A549	lung
8	chr22:31688800-31691400	Weak transcription	HMEC	breast
9	chr22:31688800-31691600	Weak transcription	Psoas Muscle	Psoas
10	chr22:31688800-31692000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr22:31688800-31692000	Weak transcription	Colonic Mucosa	Colon
12	chr22:31688800-31692400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr22:31688800-31692400	Weak transcription	Fetal Lung	lung
14	chr22:31688800-31693000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr22:31689000-31691400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr22:31689000-31691400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr22:31689000-31691600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr22:31689000-31691600	Enhancers	GM12878-XiMat	blood
19	chr22:31689000-31691800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr22:31689000-31696400	Weak transcription	HepG2	liver
21	chr22:31689200-31690600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr22:31689200-31690600	Enhancers	Stomach Smooth Muscle	stomach
23	chr22:31689200-31690800	Enhancers	Rectal Smooth Muscle	rectum
24	chr22:31689200-31691400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr22:31689200-31691400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr22:31689200-31691400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr22:31689200-31691400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr22:31689200-31691400	Weak transcription	Brain Angular Gyrus	brain
29	chr22:31689200-31691400	Weak transcription	Brain Substantia Nigra	brain
30	chr22:31689200-31691600	Weak transcription	Brain Anterior Caudate	brain
31	chr22:31689200-31692600	Enhancers	Primary B cells from cord blood	blood
32	chr22:31689200-31693000	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr22:31689200-31696400	Weak transcription	Liver	Liver
34	chr22:31689200-31696400	Weak transcription	Right Atrium	heart
35	chr22:31689400-31691400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr22:31689400-31691600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr22:31689400-31709000	Weak transcription	Placenta	Placenta
38	chr22:31689600-31690800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr22:31689600-31690800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr22:31689600-31691400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr22:31689600-31691400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr22:31689600-31692000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr22:31689800-31690800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr22:31689800-31691200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr22:31689800-31691200	Weak transcription	NHEK	skin
46	chr22:31689800-31691400	Weak transcription	Adipose Nuclei	Adipose
47	chr22:31689800-31691400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr22:31689800-31691400	Weak transcription	HSMM	muscle
49	chr22:31689800-31691400	Weak transcription	NHDF-Ad	bronchial
50	chr22:31689800-31691600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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