Variant report

Variant	rs11678350
Chromosome Location	chr2:101205999-101206000
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1052117	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1114285	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11694047	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12616005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1401753	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1533655	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1589246	1.00[JPT][hapmap]
rs17024338	1.00[JPT][hapmap]
rs2139402	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2309846	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2946584	0.82[ASN][1000 genomes]
rs2946586	0.82[ASN][1000 genomes]
rs2946587	0.82[ASN][1000 genomes]
rs2946588	0.82[ASN][1000 genomes]
rs2970994	0.82[ASN][1000 genomes]
rs2970997	1.00[JPT][hapmap]
rs2971007	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4851332	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs4851333	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs4851340	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851343	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4851344	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6542968	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6542969	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6747613	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6753993	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs68147667	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72827222	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7575538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7578708	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7594904	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7595492	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9646943	0.90[ASN][1000 genomes]

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	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv582531	chr2:100908508-101207639	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv916792	chr2:101021066-101525200	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv582532	chr2:101029002-101531943	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv834312	chr2:101044438-101238166	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11678350	LONRF2	cis	parietal	SCAN
rs11678350	NCALD	trans	lymphoblastoid	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:101194800-101206200	Weak transcription	Pancreas	Pancrea
2	chr2:101202000-101210200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr2:101202000-101210600	Weak transcription	Primary T cells from cord blood	blood
4	chr2:101204200-101206200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:101204200-101206200	Enhancers	K562	blood
6	chr2:101205000-101206000	Weak transcription	A549	lung
7	chr2:101205000-101206000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr2:101205000-101206200	Weak transcription	GM12878-XiMat	blood
9	chr2:101205000-101210600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr2:101205200-101210000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr2:101205200-101211000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:101205800-101206400	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr2:101205800-101206400	Enhancers	Placenta	Placenta
14	chr2:101205800-101206400	Enhancers	Spleen	Spleen
15	chr2:101205800-101210200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr2:101205800-101210400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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