Variant report

Variant	rs2309821
Chromosome Location	chr2:100900304-100900305
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:100893699..100897169-chr2:100899587..100903259,4	MCF-7	breast:
2	chr2:100898902..100903882-chr2:100937164..100940384,5	K562	blood:
3	chr2:100899535..100901575-chr2:100909309..100912532,4	K562	blood:
4	chr2:100899904..100902049-chr2:100905523..100907621,2	MCF-7	breast:
5	chr2:100898914..100902025-chr2:100905240..100908498,4	K562	blood:
6	chr2:100889953..100892451-chr2:100898543..100901501,2	K562	blood:

Variant related genes	Relation type
ENSG00000170500	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10865038	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10865039	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11123825	0.81[EUR][1000 genomes]
rs12464505	1.00[JPT][hapmap]
rs12467008	1.00[JPT][hapmap]
rs13008568	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13024601	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13031270	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13031493	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13031712	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13033057	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2033748	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2033749	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2309815	1.00[JPT][hapmap]
rs2309817	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2309818	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]
rs2309819	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]
rs2309820	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2309822	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2309823	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2309824	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2309825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309826	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2871341	1.00[JPT][hapmap]
rs4851281	1.00[JPT][hapmap]
rs4851282	1.00[JPT][hapmap]
rs4851284	0.82[EUR][1000 genomes]
rs4851285	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4851286	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4851287	0.89[CEU][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6542923	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6542924	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6754867	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6755791	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7421891	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7557575	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7557660	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7557977	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7559464	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7562372	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7582180	0.89[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7588623	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]
rs7601442	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7601873	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7606277	0.85[EUR][1000 genomes]
rs7607170	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7607676	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7609376	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[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	esv1803417	chr2:100898843-100901948	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2309821	LONRF2	cis	cerebellum	SCAN
rs2309821	LONRF2	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100885600-100902000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr2:100887800-100901800	Weak transcription	Fetal Intestine Small	intestine
3	chr2:100891800-100907600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:100892000-100902000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:100892000-100904000	Weak transcription	Gastric	stomach
6	chr2:100892200-100909800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:100892400-100900600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:100894400-100900400	Weak transcription	Brain Anterior Caudate	brain
9	chr2:100896600-100907000	Weak transcription	Spleen	Spleen
10	chr2:100896600-100907600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:100897600-100903600	Enhancers	Dnd41	blood
12	chr2:100898400-100900400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:100898400-100902000	Weak transcription	Fetal Stomach	stomach
14	chr2:100898400-100906800	Weak transcription	Placenta	Placenta
15	chr2:100898400-100908200	Weak transcription	Fetal Lung	lung
16	chr2:100898400-100915600	Weak transcription	Right Atrium	heart
17	chr2:100898600-100901000	Genic enhancers	K562	blood
18	chr2:100898600-100901600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr2:100898600-100902200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:100898600-100902600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:100898800-100900600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:100898800-100901800	Weak transcription	Fetal Kidney	kidney
23	chr2:100898800-100902000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr2:100898800-100902000	Weak transcription	Lung	lung
25	chr2:100898800-100903000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:100898800-100915000	Weak transcription	Adipose Nuclei	Adipose
27	chr2:100899000-100900600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr2:100899000-100901600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:100899000-100901800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:100899000-100901800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr2:100899000-100902000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr2:100899000-100902000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr2:100899000-100902200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:100899000-100907400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr2:100899200-100902000	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr2:100899400-100902400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:100899400-100903200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:100899600-100902600	Weak transcription	Small Intestine	intestine
39	chr2:100900000-100900400	Strong transcription	A549	lung
40	chr2:100900000-100900800	Strong transcription	Stomach Smooth Muscle	stomach
41	chr2:100900000-100901000	Strong transcription	Fetal Brain Male	brain
42	chr2:100900000-100903600	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr2:100900000-100904200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:100900000-100905600	Strong transcription	Aorta	Aorta
45	chr2:100900200-100900400	Strong transcription	Brain Hippocampus Middle	brain
46	chr2:100900200-100900600	Transcr. at gene 5' and 3'	Brain Angular Gyrus	brain
47	chr2:100900200-100900600	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr2:100900200-100900800	Genic enhancers	Brain Cingulate Gyrus	brain
49	chr2:100900200-100900800	ZNF genes & repeats	Brain Substantia Nigra	brain
50	chr2:100900200-100900800	Strong transcription	Pancreatic Islets	Pancreatic Islet

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