Variant report

Variant	rs62465037
Chromosome Location	chr7:66722612-66722613
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TYW1-4	chr7:66722483-66722927	NONHSAT121264

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11971398	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12530782	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12535651	0.97[EUR][1000 genomes]
rs12539705	0.88[ASN][1000 genomes]
rs12540794	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17144570	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4717359	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62465002	0.82[AMR][1000 genomes]
rs62465013	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62465014	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62465017	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62465038	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62465040	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465044	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465047	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]

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	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv888330	chr7:66502171-66877880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
4	nsv1032237	chr7:66644492-66785029	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv970518	chr7:66647675-66742783	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1027702	chr7:66722103-66841913	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
7	nsv1031048	chr7:66722103-66844039	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62465037	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66667800-66738400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:66694800-66766600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr7:66701600-66766600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr7:66705000-66724400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr7:66717400-66726400	Weak transcription	HSMMtube	muscle
6	chr7:66717400-66766200	Weak transcription	Fetal Muscle Leg	muscle
7	chr7:66717400-66766400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr7:66717600-66732800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr7:66717600-66735400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr7:66717600-66756200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr7:66717800-66766400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr7:66718800-66735200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr7:66719000-66732800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:66719000-66766400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr7:66719600-66730600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr7:66719800-66766200	Weak transcription	Spleen	Spleen
17	chr7:66720400-66724600	Weak transcription	Fetal Stomach	stomach
18	chr7:66720400-66726200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr7:66720800-66725200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr7:66721800-66756000	Weak transcription	Fetal Intestine Small	intestine
21	chr7:66722000-66723000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr7:66722400-66740600	Weak transcription	Primary T cells from cord blood	blood
23	chr7:66722600-66722800	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr7:66722600-66722800	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr7:66722600-66723000	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr7:66722600-66723000	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr7:66722600-66723200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr7:66722600-66723200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr7:66722600-66723200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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