Variant report

Variant	rs2309818
Chromosome Location	chr2:100898634-100898635
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:100896929..100899724-chr2:100932462..100934829,2	K562	blood:
2	chr2:100895235..100899399-chr2:100936905..100939740,4	K562	blood:
3	chr2:100889062..100891590-chr2:100897869..100900179,3	MCF-7	breast:
4	chr2:100889953..100892451-chr2:100898543..100901501,2	K562	blood:

Variant related genes	Relation type
ENSG00000170500	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10865038	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10865039	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11123825	0.80[EUR][1000 genomes]
rs12464505	1.00[JPT][hapmap]
rs12467008	1.00[JPT][hapmap]
rs13008568	0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13024601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13031270	0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13031493	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13031712	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13033057	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033748	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2033749	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2309815	1.00[JPT][hapmap]
rs2309817	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2309819	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309821	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2309822	0.96[CEU][hapmap];0.81[CHD][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2309823	0.96[CEU][hapmap];0.81[CHD][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2309824	0.96[CEU][hapmap];0.81[CHD][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2309825	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2309826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2871341	1.00[JPT][hapmap]
rs4851281	1.00[JPT][hapmap]
rs4851282	1.00[JPT][hapmap]
rs4851284	0.81[EUR][1000 genomes]
rs4851285	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4851286	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4851287	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6542923	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs6542924	0.81[CEU][hapmap]
rs6754867	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs6755791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7421891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7557575	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7557660	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7557977	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559464	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7562372	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7582180	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7588623	0.88[CEU][hapmap];0.81[CHD][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7601442	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7606277	0.84[EUR][1000 genomes]
rs7607170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7607676	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7609376	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][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	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	nsv834311	chr2:100816917-100990036	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2309818	LONRF2	cis	parietal	SCAN
rs2309818	LONRF2	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100879400-100900200	Weak transcription	Brain Substantia Nigra	brain
2	chr2:100884200-100900200	Weak transcription	Brain Angular Gyrus	brain
3	chr2:100885600-100902000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:100887000-100900200	Weak transcription	Left Ventricle	heart
5	chr2:100887800-100901800	Weak transcription	Fetal Intestine Small	intestine
6	chr2:100889400-100900200	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:100890600-100900200	Weak transcription	Right Ventricle	heart
8	chr2:100891400-100900000	Weak transcription	Aorta	Aorta
9	chr2:100891800-100900200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:100891800-100907600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:100892000-100902000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:100892000-100904000	Weak transcription	Gastric	stomach
13	chr2:100892200-100900200	Weak transcription	Pancreas	Pancrea
14	chr2:100892200-100909800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:100892400-100900600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr2:100894400-100900400	Weak transcription	Brain Anterior Caudate	brain
17	chr2:100895600-100900200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:100896600-100899000	Enhancers	H1 Cell Line	embryonic stem cell
19	chr2:100896600-100900000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr2:100896600-100907000	Weak transcription	Spleen	Spleen
21	chr2:100896600-100907600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:100896800-100898800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:100897400-100898800	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr2:100897400-100899000	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr2:100897400-100899000	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr2:100897600-100899000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:100897600-100899000	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr2:100897600-100903600	Enhancers	Dnd41	blood
29	chr2:100897800-100898800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:100897800-100898800	Enhancers	NH-A	brain
31	chr2:100898000-100898800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:100898000-100898800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:100898000-100899000	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr2:100898200-100898800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:100898200-100899000	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr2:100898400-100898800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:100898400-100898800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:100898400-100898800	Enhancers	Adipose Nuclei	Adipose
39	chr2:100898400-100898800	Enhancers	Fetal Kidney	kidney
40	chr2:100898400-100898800	Strong transcription	A549	lung
41	chr2:100898400-100899000	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr2:100898400-100899000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:100898400-100899000	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr2:100898400-100899000	Enhancers	Pancreatic Islets	Pancreatic Islet
45	chr2:100898400-100899400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:100898400-100900000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:100898400-100900400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:100898400-100902000	Weak transcription	Fetal Stomach	stomach
49	chr2:100898400-100906800	Weak transcription	Placenta	Placenta
50	chr2:100898400-100908200	Weak transcription	Fetal Lung	lung

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