Variant report

Variant	rs1427976
Chromosome Location	chr5:111540769-111540770
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:111540327..111540866-chr8:53311824..53312642,2	MCF-7	breast:
2	chr5:111495904..111497786-chr5:111539852..111541904,2	K562	blood:

Variant related genes	Relation type
ENSG00000224032	Chromatin interaction
ENSG00000238363	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10463628	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs11948718	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11952407	1.00[AMR][1000 genomes]
rs11954056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11954058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1427977	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17134169	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17134172	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17134175	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17134215	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs17134220	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17134247	0.87[LWK][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17134248	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4331945	1.00[AMR][1000 genomes]
rs4354094	1.00[AMR][1000 genomes]
rs4355564	1.00[AMR][1000 genomes]
rs4604230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4958016	0.81[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4958017	0.91[LWK][hapmap];0.84[MKK][hapmap];0.81[YRI][hapmap]
rs4998734	1.00[AMR][1000 genomes]
rs6594579	0.91[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599367	chr5:110924280-111602713	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv948869	chr5:111476404-111695183	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv531291	chr5:111497440-111756788	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription 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	19 gene(s)	inside rSNPs	diseases
7	nsv599371	chr5:111519018-111676755	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1427976	TRAT1	trans	lymphoblastoid	seeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111501400-111546400	Weak transcription	Spleen	Spleen
2	chr5:111502400-111546400	Weak transcription	Aorta	Aorta
3	chr5:111502800-111546000	Weak transcription	Ovary	ovary
4	chr5:111504800-111541400	Weak transcription	Right Ventricle	heart
5	chr5:111504800-111557800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:111504800-111586400	Weak transcription	Gastric	stomach
7	chr5:111505600-111541800	Weak transcription	Fetal Muscle Leg	muscle
8	chr5:111510800-111547400	Weak transcription	HUVEC	blood vessel
9	chr5:111519000-111546400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:111519200-111553800	Weak transcription	Pancreas	Pancrea
11	chr5:111519800-111553600	Weak transcription	Esophagus	oesophagus
12	chr5:111529800-111553600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr5:111535000-111541800	Weak transcription	Fetal Brain Female	brain
14	chr5:111536400-111541600	Weak transcription	Fetal Stomach	stomach
15	chr5:111538000-111541800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr5:111538000-111553400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr5:111538200-111543200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr5:111538200-111546400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr5:111538400-111540800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr5:111538600-111541400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr5:111538600-111541800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:111538600-111544800	Weak transcription	Fetal Kidney	kidney
23	chr5:111538600-111563600	Weak transcription	Lung	lung
24	chr5:111538800-111541600	Weak transcription	Adipose Nuclei	Adipose
25	chr5:111538800-111541600	Weak transcription	Left Ventricle	heart
26	chr5:111539000-111553600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:111539400-111553200	Weak transcription	NHEK	skin
28	chr5:111540000-111541000	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr5:111540000-111541200	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr5:111540000-111541200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr5:111540000-111541400	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr5:111540000-111541400	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr5:111540000-111541400	Enhancers	K562	blood
34	chr5:111540000-111542600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:111540200-111540800	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr5:111540200-111540800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:111540200-111541000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr5:111540200-111541000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:111540200-111541200	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr5:111540200-111542000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:111540400-111544400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr5:111540400-111553600	Weak transcription	Fetal Heart	heart
43	chr5:111540600-111540800	Enhancers	Hela-S3	cervix
44	chr5:111540600-111541800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr5:111540600-111542200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr5:111540600-111542400	Weak transcription	Placenta	Placenta

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