Variant report

Variant	rs4660342
Chromosome Location	chr1:46595082-46595083
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46592691..46601867-chr1:46642778..46650670,25	MCF-7	breast:
2	chr1:46593944..46606364-chr1:46632700..46654752,92	MCF-7	breast:
3	chr1:46590920..46606215-chr1:46630948..46642525,66	MCF-7	breast:
4	chr1:46539301..46542109-chr1:46593779..46595695,2	K562	blood:
5	chr1:46531892..46533650-chr1:46593425..46595448,2	MCF-7	breast:
6	chr1:46500927..46503041-chr1:46594569..46596961,2	MCF-7	breast:

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

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1085244	0.81[ASN][1000 genomes]
rs1355642	0.80[ASN][1000 genomes]
rs1707335	0.83[ASN][1000 genomes]
rs4660341	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4660911	0.81[ASN][1000 genomes]
rs6662641	0.83[ASN][1000 genomes]
rs6675726	0.81[ASN][1000 genomes]
rs785485	0.83[ASN][1000 genomes]
rs785488	0.83[ASN][1000 genomes]
rs785489	0.83[ASN][1000 genomes]
rs785491	0.83[ASN][1000 genomes]
rs785492	0.83[ASN][1000 genomes]
rs785494	0.83[ASN][1000 genomes]
rs785495	0.83[ASN][1000 genomes]
rs785498	0.84[ASN][1000 genomes]
rs785502	0.81[ASN][1000 genomes]
rs785503	0.81[ASN][1000 genomes]
rs785520	0.83[ASN][1000 genomes]
rs809774	0.83[ASN][1000 genomes]
rs9429094	0.82[ASN][1000 genomes]
rs9429189	0.83[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4660342	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs4660342	GPBP1L1	cis	Muscle Skeletal	GTEx
rs4660342	IPP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46540400-46595200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:46541200-46595800	Weak transcription	Fetal Intestine Small	intestine
3	chr1:46562400-46595800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:46567800-46595200	Weak transcription	Primary T cells from cord blood	blood
5	chr1:46574000-46595200	Weak transcription	HSMM	muscle
6	chr1:46581800-46595200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:46584600-46595200	Weak transcription	Fetal Lung	lung
8	chr1:46592200-46595200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:46593200-46595800	Weak transcription	Ovary	ovary
10	chr1:46593400-46598200	Active TSS	Right Atrium	heart
11	chr1:46593600-46595200	Enhancers	Fetal Heart	heart
12	chr1:46594000-46595200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:46594000-46599000	Active TSS	Right Ventricle	heart
14	chr1:46594000-46599200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:46594000-46599200	Active TSS	Psoas Muscle	Psoas
16	chr1:46594000-46599400	Active TSS	Left Ventricle	heart
17	chr1:46594200-46595200	Active TSS	Adipose Nuclei	Adipose
18	chr1:46594200-46595200	Enhancers	HMEC	breast
19	chr1:46594200-46595800	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:46594400-46595200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:46594400-46595200	Active TSS	GM12878-XiMat	blood
22	chr1:46594600-46595200	Enhancers	Hela-S3	cervix
23	chr1:46594600-46596000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:46594600-46596600	Weak transcription	Placenta	Placenta
25	chr1:46594600-46596800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:46594600-46599200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:46594600-46599400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:46594800-46595200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:46594800-46595200	Enhancers	Fetal Kidney	kidney
30	chr1:46594800-46595200	Enhancers	K562	blood
31	chr1:46594800-46596200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:46594800-46599200	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr1:46594800-46599400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:46595000-46595200	Enhancers	Brain Germinal Matrix	brain
35	chr1:46595000-46595200	Enhancers	Fetal Brain Male	brain
36	chr1:46595000-46595200	Active TSS	Fetal Brain Female	brain
37	chr1:46595000-46595200	Enhancers	Dnd41	blood
38	chr1:46595000-46595200	Enhancers	HUVEC	blood vessel
39	chr1:46595000-46595200	Enhancers	NH-A	brain
40	chr1:46595000-46595400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:46595000-46595800	Enhancers	Muscle Satellite Cultured Cells	--
42	chr1:46595000-46599200	Active TSS	Cortex derived primary cultured neurospheres	brain

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