Variant report

Variant	rs1416706
Chromosome Location	chr1:46602844-46602845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46602297..46604849-chr1:46618542..46621486,2	K562	blood:
2	chr1:46601377..46603890-chr1:46611538..46613763,2	MCF-7	breast:
3	chr1:46593944..46606364-chr1:46632700..46654752,92	MCF-7	breast:
4	chr1:46590920..46606215-chr1:46630948..46642525,66	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117461	Chromatin interaction
ENSG00000250719	Chromatin interaction
ENSG00000117472	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10890382	0.81[CHB][hapmap];0.85[YRI][hapmap]
rs11211232	0.89[YRI][hapmap]
rs11211235	0.81[CHB][hapmap]
rs11211236	0.81[CHB][hapmap]
rs11211237	0.83[CHB][hapmap]
rs11211243	0.81[CHB][hapmap]
rs12090501	0.84[ASN][1000 genomes]
rs1473840	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1613296	0.85[CHB][hapmap]
rs1707302	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1707303	0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs1707317	0.86[CHB][hapmap]
rs1707322	0.85[CHB][hapmap]
rs1707337	0.86[CHB][hapmap]
rs1768801	0.86[CHB][hapmap]
rs1768802	0.85[CHB][hapmap]
rs1768807	0.86[CHB][hapmap]
rs1768817	0.86[CHB][hapmap]
rs1768818	0.86[CHB][hapmap]
rs2458400	0.86[CHB][hapmap]
rs3922887	0.81[CHB][hapmap]
rs4660328	0.81[CHB][hapmap]
rs4660335	0.81[CHB][hapmap]
rs4660341	0.83[ASN][1000 genomes]
rs4660900	0.81[CHB][hapmap]
rs6429588	0.81[CHB][hapmap]
rs6661500	0.81[CHB][hapmap]
rs6677777	0.81[CHB][hapmap]
rs7538978	0.85[CHB][hapmap]
rs785465	0.85[CHB][hapmap]
rs785467	0.86[CHB][hapmap]
rs785468	0.85[CHB][hapmap]
rs785470	0.86[CHB][hapmap]
rs785475	0.89[YRI][hapmap]
rs785478	0.81[CHB][hapmap]
rs785483	0.81[ASN][1000 genomes]
rs785484	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs785486	0.84[ASN][1000 genomes]
rs785490	0.84[ASN][1000 genomes]
rs785493	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs785496	0.84[ASN][1000 genomes]
rs785497	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs785499	0.80[ASN][1000 genomes]
rs785500	0.83[ASN][1000 genomes]
rs785504	0.88[ASN][1000 genomes]
rs785506	0.86[CHB][hapmap]
rs785510	0.86[CHB][hapmap]
rs785512	0.85[CHB][hapmap]
rs785516	0.81[ASN][1000 genomes]
rs785517	0.84[ASN][1000 genomes]
rs785519	0.84[ASN][1000 genomes]
rs796773	0.82[ASN][1000 genomes]
rs925524	0.81[CHB][hapmap]
rs9429095	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised 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 miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1003517	chr1:46244432-46609881	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
6	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
7	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
8	esv2754420	chr1:46461580-46635180	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv1012418	chr1:46544842-46619890	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv534948	chr1:46544842-46619890	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
13	nsv1006530	chr1:46544842-46655484	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
14	nsv534949	chr1:46544842-46655484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1416706	GPBP1L1	cis	Lymphoblastoid	GTEx
rs1416706	Hs.396207	cis	multi-tissue	Pritchard
rs1416706	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs1416706	MAST2	cis	Artery Tibial	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46599200-46603200	Weak transcription	Ovary	ovary
2	chr1:46599400-46603200	Weak transcription	Liver	Liver
3	chr1:46599600-46603200	Weak transcription	HSMMtube	muscle
4	chr1:46599600-46604000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr1:46599800-46603200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr1:46600000-46603200	Weak transcription	HUVEC	blood vessel
7	chr1:46600000-46604000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:46600200-46603200	Weak transcription	Fetal Intestine Large	intestine
9	chr1:46600200-46603200	Weak transcription	Fetal Lung	lung
10	chr1:46600600-46603400	Weak transcription	HSMM	muscle
11	chr1:46601000-46603000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:46601000-46603200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:46601000-46603200	Weak transcription	Adipose Nuclei	Adipose
14	chr1:46601000-46603200	Weak transcription	NHLF	lung
15	chr1:46601000-46603400	Weak transcription	K562	blood
16	chr1:46601000-46603400	Weak transcription	NH-A	brain
17	chr1:46601200-46603000	Enhancers	Fetal Heart	heart
18	chr1:46601200-46603200	Weak transcription	Fetal Stomach	stomach
19	chr1:46601200-46603400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:46601400-46603200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:46601400-46603200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:46601400-46603200	Weak transcription	Osteobl	bone
23	chr1:46601400-46603400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr1:46601400-46603600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:46601600-46603200	Enhancers	Hela-S3	cervix
26	chr1:46601800-46603200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr1:46602200-46603000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:46602200-46603800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:46602200-46604000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:46602200-46604000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:46602200-46604000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:46602400-46603400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:46602400-46603600	Enhancers	Left Ventricle	heart
34	chr1:46602400-46603800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:46602400-46604000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:46602400-46604200	Enhancers	Fetal Muscle Leg	muscle
37	chr1:46602600-46603000	Weak transcription	Right Atrium	heart
38	chr1:46602600-46603800	Enhancers	Fetal Kidney	kidney
39	chr1:46602600-46604600	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links