Variant report

Variant	rs7588623
Chromosome Location	chr2:100913361-100913362
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:100912722..100916379-chr2:100917427..100921061,4	K562	blood:
2	chr2:100900693..100917248-chr2:100932005..100942326,51	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170500	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10170878	1.00[JPT][hapmap]
rs10173499	1.00[JPT][hapmap]
rs10865038	0.82[EUR][1000 genomes]
rs10865039	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123825	0.88[EUR][1000 genomes]
rs12463633	1.00[JPT][hapmap]
rs12472141	1.00[JPT][hapmap]
rs13008568	0.89[EUR][1000 genomes]
rs13024601	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13031270	0.90[EUR][1000 genomes]
rs13031493	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13031712	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13033057	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13397337	1.00[JPT][hapmap]
rs1437971	1.00[ASW][hapmap];0.83[TSI][hapmap]
rs2033748	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2033749	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2309817	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309818	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]
rs2309819	0.89[CEU][hapmap];0.81[CHD][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2309820	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2309821	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2309822	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309823	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309824	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309825	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2309826	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4851283	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4851285	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851286	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4851287	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6542919	1.00[JPT][hapmap]
rs6542923	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6542924	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs6724490	1.00[JPT][hapmap]
rs6727712	1.00[JPT][hapmap]
rs6754867	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6755791	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs7421891	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7557575	0.84[EUR][1000 genomes]
rs7557660	0.83[EUR][1000 genomes]
rs7557977	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7559464	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7582180	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7601442	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7601873	0.89[CEU][hapmap]
rs7606277	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7607170	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7607676	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7609376	0.89[CEU][hapmap];0.89[CHD][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7588623	LONRF2	cis	parietal	SCAN
rs7588623	LONRF2	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100898400-100915600	Weak transcription	Right Atrium	heart
2	chr2:100898800-100915000	Weak transcription	Adipose Nuclei	Adipose
3	chr2:100900200-100919000	Strong transcription	Fetal Brain Female	brain
4	chr2:100900800-100926600	Weak transcription	Right Ventricle	heart
5	chr2:100901000-100937000	Weak transcription	Fetal Brain Male	brain
6	chr2:100903200-100918000	Weak transcription	Liver	Liver
7	chr2:100903400-100930800	Weak transcription	Brain Substantia Nigra	brain
8	chr2:100903600-100914400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr2:100903600-100926200	Weak transcription	Fetal Kidney	kidney
10	chr2:100908000-100919400	Weak transcription	Spleen	Spleen
11	chr2:100908200-100917800	Weak transcription	Lung	lung
12	chr2:100908400-100914400	Weak transcription	Esophagus	oesophagus
13	chr2:100908400-100917600	Weak transcription	Fetal Stomach	stomach
14	chr2:100908600-100915800	Strong transcription	Stomach Smooth Muscle	stomach
15	chr2:100908800-100926600	Weak transcription	Gastric	stomach
16	chr2:100909000-100913600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:100909000-100915000	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:100909000-100920600	Weak transcription	Fetal Intestine Small	intestine
19	chr2:100909200-100913600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:100909200-100914000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:100909800-100914200	Strong transcription	Pancreas	Pancrea
22	chr2:100910200-100920000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:100910200-100920400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:100910400-100918200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:100910400-100925800	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:100910600-100915400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:100910800-100915600	Strong transcription	A549	lung
28	chr2:100910800-100917600	Weak transcription	Left Ventricle	heart
29	chr2:100910800-100933600	Weak transcription	K562	blood
30	chr2:100911000-100913800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:100911000-100915200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:100911000-100915200	Weak transcription	Hela-S3	cervix
33	chr2:100911000-100917800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:100911200-100917800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr2:100911800-100918600	Strong transcription	Brain Germinal Matrix	brain
36	chr2:100912000-100915800	Strong transcription	Ovary	ovary
37	chr2:100912000-100918200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:100912000-100919400	Strong transcription	Brain Anterior Caudate	brain
39	chr2:100912200-100915800	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr2:100912400-100917800	Weak transcription	Aorta	Aorta
41	chr2:100912400-100918600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr2:100912600-100917600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr2:100912800-100934800	Weak transcription	Brain Angular Gyrus	brain
44	chr2:100913000-100915200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr2:100913200-100915200	Weak transcription	Brain Hippocampus Middle	brain

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