Variant report

Variant	rs11123823
Chromosome Location	chr2:100916315-100916316
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:100912722..100916379-chr2:100917427..100921061,4	K562	blood:
2	chr2:100906645..100910351-chr2:100915314..100919031,3	K562	blood:
3	chr2:100900693..100917248-chr2:100932005..100942326,51	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170500	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10048665	0.83[EUR][1000 genomes]
rs10180423	0.92[CEU][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs10194210	0.87[EUR][1000 genomes]
rs10195793	0.88[EUR][1000 genomes]
rs10460478	0.87[EUR][1000 genomes]
rs11123822	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11123824	0.88[EUR][1000 genomes]
rs11123826	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs11678158	0.81[EUR][1000 genomes]
rs11680660	0.80[EUR][1000 genomes]
rs11682748	0.92[CEU][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs11683088	0.82[EUR][1000 genomes]
rs11683121	0.87[EUR][1000 genomes]
rs11684004	0.80[EUR][1000 genomes]
rs11685250	0.80[EUR][1000 genomes]
rs11685491	1.00[YRI][hapmap]
rs11686293	0.89[EUR][1000 genomes]
rs11686799	0.80[EUR][1000 genomes]
rs11686842	0.80[EUR][1000 genomes]
rs11686880	0.80[EUR][1000 genomes]
rs11687241	1.00[YRI][hapmap]
rs11687352	0.87[EUR][1000 genomes]
rs11689199	1.00[YRI][hapmap]
rs11689201	1.00[YRI][hapmap]
rs11689439	0.88[EUR][1000 genomes]
rs11691135	0.81[EUR][1000 genomes]
rs11691684	0.84[EUR][1000 genomes]
rs11693044	0.89[EUR][1000 genomes]
rs11693424	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs11694642	0.80[EUR][1000 genomes]
rs11694700	0.81[EUR][1000 genomes]
rs11694723	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs11695996	1.00[YRI][hapmap]
rs11892034	0.81[EUR][1000 genomes]
rs12612755	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12615466	0.89[EUR][1000 genomes]
rs12617779	0.81[EUR][1000 genomes]
rs12622318	0.89[EUR][1000 genomes]
rs12712075	0.88[EUR][1000 genomes]
rs12989897	0.81[EUR][1000 genomes]
rs12990688	0.87[EUR][1000 genomes]
rs12991172	0.81[EUR][1000 genomes]
rs12994592	1.00[YRI][hapmap]
rs12999151	0.81[EUR][1000 genomes]
rs12999779	0.88[EUR][1000 genomes]
rs13001423	0.88[EUR][1000 genomes]
rs13006224	0.90[EUR][1000 genomes]
rs13019179	1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13020451	0.88[EUR][1000 genomes]
rs13023534	0.88[EUR][1000 genomes]
rs13026570	0.81[EUR][1000 genomes]
rs13031711	0.81[EUR][1000 genomes]
rs13031906	0.81[EUR][1000 genomes]
rs1530028	0.92[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs1866198	0.88[EUR][1000 genomes]
rs1946799	0.81[EUR][1000 genomes]
rs1967339	0.87[EUR][1000 genomes]
rs1967341	0.88[EUR][1000 genomes]
rs2067783	0.85[CEU][hapmap];0.84[MEX][hapmap]
rs2164847	0.80[EUR][1000 genomes]
rs2871340	0.86[JPT][hapmap]
rs4264577	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs4438499	0.86[JPT][hapmap]
rs4477940	0.80[EUR][1000 genomes]
rs4622752	1.00[ASW][hapmap];0.88[CEU][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4851267	1.00[YRI][hapmap]
rs4851288	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs4851292	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs4851293	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs4851294	0.81[EUR][1000 genomes]
rs6716636	0.81[EUR][1000 genomes]
rs6723909	0.86[JPT][hapmap]
rs6725052	0.81[EUR][1000 genomes]
rs6731549	0.81[EUR][1000 genomes]
rs74177696	0.80[EUR][1000 genomes]
rs7425449	0.92[CEU][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs7425797	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs7571306	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7597615	0.80[EUR][1000 genomes]
rs764828	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs920269	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs920270	0.88[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11123823	LONRF2	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100900200-100919000	Strong transcription	Fetal Brain Female	brain
2	chr2:100900800-100926600	Weak transcription	Right Ventricle	heart
3	chr2:100901000-100937000	Weak transcription	Fetal Brain Male	brain
4	chr2:100903200-100918000	Weak transcription	Liver	Liver
5	chr2:100903400-100930800	Weak transcription	Brain Substantia Nigra	brain
6	chr2:100903600-100926200	Weak transcription	Fetal Kidney	kidney
7	chr2:100908000-100919400	Weak transcription	Spleen	Spleen
8	chr2:100908200-100917800	Weak transcription	Lung	lung
9	chr2:100908400-100917600	Weak transcription	Fetal Stomach	stomach
10	chr2:100908800-100926600	Weak transcription	Gastric	stomach
11	chr2:100909000-100920600	Weak transcription	Fetal Intestine Small	intestine
12	chr2:100910200-100920000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:100910200-100920400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:100910400-100918200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:100910400-100925800	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:100910800-100917600	Weak transcription	Left Ventricle	heart
17	chr2:100910800-100933600	Weak transcription	K562	blood
18	chr2:100911000-100917800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:100911200-100917800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:100911800-100918600	Strong transcription	Brain Germinal Matrix	brain
21	chr2:100912000-100918200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:100912000-100919400	Strong transcription	Brain Anterior Caudate	brain
23	chr2:100912400-100917800	Weak transcription	Aorta	Aorta
24	chr2:100912400-100918600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr2:100912600-100917600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr2:100912800-100934800	Weak transcription	Brain Angular Gyrus	brain
27	chr2:100914200-100917600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:100914200-100917600	Weak transcription	Pancreas	Pancrea
29	chr2:100914400-100918400	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr2:100915000-100916600	Strong transcription	Colon Smooth Muscle	Colon
31	chr2:100915400-100919800	Weak transcription	Adipose Nuclei	Adipose
32	chr2:100915600-100916400	Weak transcription	A549	lung
33	chr2:100915800-100917000	Weak transcription	Ovary	ovary
34	chr2:100915800-100917800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr2:100915800-100923600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr2:100915800-100930600	Weak transcription	Brain Hippocampus Middle	brain
37	chr2:100916000-100923600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr2:100916200-100917800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:100916200-100917800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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