Variant report

Variant	rs13217373
Chromosome Location	chr6:119816636-119816637
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAN1A1-2	chr6:119816057-119818057	ucscGeneNc_uc003pyn_1

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10457355	0.84[CEU][hapmap]
rs10485001	0.80[MEX][hapmap]
rs10485004	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10485005	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153832	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11759899	0.80[MEX][hapmap]
rs12195793	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12197734	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201876	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203478	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206086	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206472	0.84[CEU][hapmap]
rs12207914	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208820	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209160	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13194194	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13201608	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13201736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13208284	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1499571	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17628078	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17628412	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17628430	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17628459	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17628530	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2133533	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2153824	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62418722	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62418723	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62418738	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62418739	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66623281	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6899913	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915559	0.87[MEX][hapmap]
rs6915947	0.87[MEX][hapmap]
rs6918348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918913	0.87[MEX][hapmap]
rs6919823	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923308	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6923537	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923854	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6927955	0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6935126	0.84[CEU][hapmap];0.94[MEX][hapmap]
rs72954953	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743821	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7753315	0.87[MEX][hapmap]
rs7754482	0.84[CEU][hapmap];0.87[MEX][hapmap]
rs7756933	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7774848	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs870891	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926859	0.81[CEU][hapmap]
rs9489686	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1027904	chr6:119709488-120001986	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv533518	chr6:119712186-119998618	ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3442553	chr6:119742069-120076777	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv5455	chr6:119794976-119839636	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13217373	FAM162B	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119814600-119817200	Enhancers	Stomach Mucosa	stomach
2	chr6:119814800-119816800	Enhancers	HepG2	liver
3	chr6:119815200-119817000	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr6:119815200-119817200	Enhancers	Fetal Intestine Small	intestine
5	chr6:119815200-119817200	Enhancers	Pancreas	Pancrea
6	chr6:119815200-119817200	Enhancers	Small Intestine	intestine
7	chr6:119815200-119817400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr6:119815200-119817400	Enhancers	Fetal Intestine Large	intestine
9	chr6:119815600-119816800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:119815600-119817000	Enhancers	Gastric	stomach
11	chr6:119815600-119817200	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr6:119815600-119817400	Enhancers	Duodenum Mucosa	Duodenum
13	chr6:119815600-119818800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr6:119815800-119817400	Enhancers	Left Ventricle	heart
15	chr6:119815800-119819000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:119816000-119816800	Weak transcription	Spleen	Spleen
17	chr6:119816200-119817400	Enhancers	Liver	Liver
18	chr6:119816200-119818000	Enhancers	Fetal Heart	heart
19	chr6:119816600-119816800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr6:119816600-119816800	Enhancers	Fetal Thymus	thymus

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