Variant report

Variant	rs4723891
Chromosome Location	chr7:39742677-39742678
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:39739429..39741292-chr7:39741440..39743225,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C7orf11-4	chr7:39742579-39742895	ENSG00000228554.1

Variant related genes	Relation type
ENSG00000006451	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11769865	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11982634	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2107710	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2158548	0.89[EUR][1000 genomes]
rs2158549	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2189837	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237499	0.82[ASN][1000 genomes]
rs2329464	0.93[EUR][1000 genomes]
rs2876862	0.89[EUR][1000 genomes]
rs3823742	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4723887	0.89[EUR][1000 genomes]
rs4723892	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6462936	0.83[EUR][1000 genomes]
rs6462937	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6952363	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6952866	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6956681	0.93[EUR][1000 genomes]
rs6961667	0.89[EUR][1000 genomes]
rs6969070	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6969523	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7785049	0.89[EUR][1000 genomes]
rs7806651	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs917077	0.88[EUR][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	nsv508451	chr7:39660784-39787222	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv887971	chr7:39662268-39745775	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv427777	chr7:39726513-39936904	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4723891	LINC00265	cis	Thyroid	GTEx
rs4723891	LINC00265	cis	lung	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39715200-39749400	Weak transcription	Aorta	Aorta
2	chr7:39723600-39742800	Weak transcription	Brain Angular Gyrus	brain
3	chr7:39723800-39743000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:39726600-39742800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr7:39727400-39747800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:39730600-39749200	Weak transcription	Ovary	ovary
7	chr7:39732000-39748000	Strong transcription	HUVEC	blood vessel
8	chr7:39732000-39749200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr7:39734200-39746200	Weak transcription	Fetal Kidney	kidney
10	chr7:39734600-39743000	Strong transcription	HSMM	muscle
11	chr7:39735600-39743200	Strong transcription	Primary B cells from cord blood	blood
12	chr7:39735600-39743400	Strong transcription	Primary T cells from cord blood	blood
13	chr7:39736000-39743600	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr7:39736600-39749400	Weak transcription	Fetal Heart	heart
15	chr7:39737200-39743000	Weak transcription	Brain Hippocampus Middle	brain
16	chr7:39737400-39742800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr7:39737400-39743800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr7:39737400-39749800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr7:39737600-39742800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr7:39737600-39743200	Strong transcription	NHDF-Ad	bronchial
21	chr7:39737600-39748800	Weak transcription	Colon Smooth Muscle	Colon
22	chr7:39737800-39749400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr7:39737800-39749400	Weak transcription	Psoas Muscle	Psoas
24	chr7:39738000-39748600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:39738000-39749200	Weak transcription	Fetal Brain Female	brain
26	chr7:39738000-39749400	Weak transcription	Placenta	Placenta
27	chr7:39738400-39743600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr7:39738400-39744400	Weak transcription	HepG2	liver
29	chr7:39738400-39748400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr7:39738600-39744600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr7:39738600-39748800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr7:39738600-39748800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr7:39738600-39749200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr7:39739600-39743000	Weak transcription	K562	blood
35	chr7:39739600-39749600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr7:39740000-39743200	Enhancers	Stomach Mucosa	stomach
37	chr7:39740200-39744800	Weak transcription	Brain Substantia Nigra	brain
38	chr7:39740200-39746200	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr7:39740200-39747200	Weak transcription	Gastric	stomach
40	chr7:39740200-39748000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr7:39740200-39749200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr7:39740200-39749400	Weak transcription	Pancreas	Pancrea
43	chr7:39740200-39749400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr7:39740200-39749600	Weak transcription	Lung	lung
45	chr7:39740200-39752000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr7:39740400-39745000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr7:39740400-39745600	Weak transcription	Esophagus	oesophagus
48	chr7:39740400-39747400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr7:39740400-39749000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr7:39740400-39749600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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