Variant report

Variant	rs4142284
Chromosome Location	chr7:107940173-107940174
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:107939868..107942167-chr7:107945482..107947094,2	MCF-7	breast:
2	chr7:107938518..107941105-chr7:107997657..107999533,3	MCF-7	breast:
3	chr7:107885444..107889446-chr7:107936320..107941216,4	MCF-7	breast:
4	chr7:107938640..107940703-chr7:107991452..107994655,4	MCF-7	breast:
5	chr7:107937668..107941473-chr7:107996254..108000894,5	MCF-7	breast:
6	chr7:107938795..107940686-chr7:107979875..107982816,2	MCF-7	breast:
7	chr7:107840057..107842255-chr7:107937956..107941774,3	MCF-7	breast:
8	chr7:107940013..107942705-chr7:108208035..108210155,2	K562	blood:
9	chr7:107938387..107941926-chr7:108096111..108098470,4	MCF-7	breast:
10	chr7:107925805..107928742-chr7:107940005..107942470,2	K562	blood:
11	chr7:107936793..107941797-chr7:107984945..107993863,13	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000128590	Chromatin interaction
ENSG00000135241	Chromatin interaction
ENSG00000177683	Chromatin interaction
ENSG00000091129	Chromatin interaction
ENSG00000266112	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12671060	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13225168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13242382	0.80[ASN][1000 genomes]
rs17155421	0.83[LWK][hapmap]
rs2111201	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2111202	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2267883	0.83[CHB][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs2267884	0.84[JPT][hapmap]
rs2267887	0.83[CHB][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs4727706	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7800100	0.82[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap]
rs7807435	0.83[AFR][1000 genomes]
rs9649300	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv949344	chr7:107396502-107987085	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv831090	chr7:107786650-108011196	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv888942	chr7:107893695-108055858	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv888943	chr7:107893695-108058574	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv1030425	chr7:107910716-108041036	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1019059	chr7:107935905-107995523	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv1021783	chr7:107935905-107998281	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	esv2761354	chr7:107935905-107998293	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv1031824	chr7:107935905-108006038	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv1017288	chr7:107939739-108000837	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4142284	LRRN3	cis	cerebellum	SCAN
rs4142284	NME3	trans	cerebellum	SCAN
rs4142284	CDHR3	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107925400-107952000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:107931000-107947400	Weak transcription	Fetal Brain Female	brain
3	chr7:107932000-107950600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr7:107933400-107942800	Weak transcription	Brain Angular Gyrus	brain
5	chr7:107933600-107947400	Weak transcription	Brain Hippocampus Middle	brain
6	chr7:107935200-107947000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr7:107935400-107950600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr7:107936600-107946800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:107938000-107942600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr7:107938200-107941600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr7:107938400-107940400	Enhancers	Placenta	Placenta
12	chr7:107938400-107941000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:107939200-107940400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr7:107939200-107940600	Enhancers	HMEC	breast
15	chr7:107939200-107940600	Enhancers	NH-A	brain
16	chr7:107939600-107940400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:107939600-107940400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr7:107939600-107940400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr7:107939600-107940400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr7:107939600-107940400	Enhancers	Brain Substantia Nigra	brain
21	chr7:107939600-107940400	Enhancers	HSMM	muscle
22	chr7:107939600-107940400	Enhancers	HSMMtube	muscle
23	chr7:107939600-107940400	Enhancers	NHEK	skin
24	chr7:107939600-107940400	Enhancers	Osteobl	bone
25	chr7:107939600-107940600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:107939600-107940600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr7:107939600-107940600	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr7:107939600-107940600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr7:107939600-107940600	Enhancers	Fetal Intestine Large	intestine
30	chr7:107939600-107940600	Flanking Active TSS	A549	lung
31	chr7:107939600-107942800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:107939800-107940200	Weak transcription	Pancreas	Pancrea
33	chr7:107939800-107940400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr7:107939800-107940400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr7:107939800-107940400	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr7:107939800-107940600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr7:107939800-107940600	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr7:107939800-107941200	Enhancers	Fetal Intestine Small	intestine
39	chr7:107940000-107940200	Enhancers	Brain Cingulate Gyrus	brain
40	chr7:107940000-107940200	Flanking Active TSS	HUVEC	blood vessel
41	chr7:107940000-107940600	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr7:107940000-107940600	Enhancers	Hela-S3	cervix
43	chr7:107940000-107943600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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