Variant report

Variant	rs12702393
Chromosome Location	chr7:47845411-47845412
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12702392	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13231277	0.88[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13239205	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13241400	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs13246591	0.80[CEU][hapmap];0.87[CHD][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs17131825	0.80[CEU][hapmap];0.87[CHD][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs17131827	0.89[CEU][hapmap]
rs17545682	0.80[CEU][hapmap];0.81[TSI][hapmap]
rs34712849	0.82[EUR][1000 genomes]
rs35030912	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6946880	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6946939	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970132	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6979746	0.81[LWK][hapmap]
rs73103467	0.82[EUR][1000 genomes]
rs7780916	0.80[CEU][hapmap]
rs7802098	0.80[CEU][hapmap];0.87[TSI][hapmap]

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	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv888003	chr7:47694270-47907214	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12702393	SNORA5C	cis	parietal	SCAN
rs12702393	TMED4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47817200-47846600	Weak transcription	Left Ventricle	heart
2	chr7:47823400-47847200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr7:47823400-47849400	Weak transcription	Psoas Muscle	Psoas
4	chr7:47823400-47852200	Weak transcription	Right Ventricle	heart
5	chr7:47827000-47851400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:47827600-47845800	Weak transcription	Fetal Stomach	stomach
7	chr7:47834400-47847000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr7:47835400-47845800	Weak transcription	Colon Smooth Muscle	Colon
9	chr7:47838400-47853600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr7:47838800-47847800	Enhancers	HepG2	liver
11	chr7:47839200-47845800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:47840800-47847400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr7:47842000-47846600	Enhancers	Fetal Intestine Small	intestine
14	chr7:47842200-47846600	Weak transcription	HMEC	breast
15	chr7:47842400-47846600	Weak transcription	Esophagus	oesophagus
16	chr7:47842600-47852000	Weak transcription	Gastric	stomach
17	chr7:47843200-47846800	Enhancers	HSMM	muscle
18	chr7:47843400-47846000	Enhancers	A549	lung
19	chr7:47844200-47845600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr7:47844400-47846400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr7:47844400-47846800	Enhancers	NHLF	lung
22	chr7:47844400-47847400	Enhancers	HUVEC	blood vessel
23	chr7:47844400-47848400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr7:47844600-47847400	Enhancers	Ovary	ovary
25	chr7:47844600-47848000	Enhancers	Spleen	Spleen
26	chr7:47845000-47845600	Weak transcription	HSMMtube	muscle
27	chr7:47845000-47845800	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr7:47845000-47846200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr7:47845000-47846400	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr7:47845000-47846400	Enhancers	Right Atrium	heart
31	chr7:47845000-47846400	Weak transcription	Osteobl	bone
32	chr7:47845000-47846600	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr7:47845000-47846800	Enhancers	Fetal Intestine Large	intestine
34	chr7:47845000-47848200	Enhancers	Lung	lung
35	chr7:47845200-47846400	Enhancers	Adipose Nuclei	Adipose
36	chr7:47845200-47846600	Weak transcription	NHEK	skin
37	chr7:47845200-47847800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr7:47845200-47847800	Enhancers	Pancreas	Pancrea
39	chr7:47845400-47846600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr7:47845400-47846800	Enhancers	Aorta	Aorta
41	chr7:47845400-47847000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr7:47845400-47847400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr7:47845400-47847400	Enhancers	Fetal Heart	heart

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