Variant report

Variant	rs4622752
Chromosome Location	chr2:100892018-100892019
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:100887684..100889414-chr2:100891922..100893717,2	K562	blood:
2	chr2:100889734..100892387-chr2:100894047..100896646,2	K562	blood:
3	chr2:100889401..100893026-chr2:100904259..100909793,5	MCF-7	breast:
4	chr2:100891457..100894388-chr2:100906302..100910364,4	K562	blood:
5	chr2:100886067..100888697-chr2:100889911..100892132,2	MCF-7	breast:
6	chr2:100880887..100882514-chr2:100890263..100892198,2	MCF-7	breast:
7	chr2:100889953..100892451-chr2:100898543..100901501,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10180423	0.88[CEU][hapmap]
rs10496346	0.81[AFR][1000 genomes]
rs11123818	0.81[AFR][1000 genomes]
rs11123821	0.81[AFR][1000 genomes]
rs11123822	0.87[EUR][1000 genomes]
rs11123823	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]
rs11682748	0.88[CEU][hapmap]
rs11685491	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs11687241	1.00[YRI][hapmap]
rs11689199	1.00[YRI][hapmap]
rs11689201	1.00[YRI][hapmap]
rs11693424	0.88[CEU][hapmap]
rs11694723	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11695996	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs12053126	0.81[AFR][1000 genomes]
rs12612755	0.83[EUR][1000 genomes]
rs12615145	0.81[AFR][1000 genomes]
rs12994592	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs13010010	0.81[AFR][1000 genomes]
rs13019179	0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1530028	0.88[CEU][hapmap]
rs2067783	0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2309812	0.81[AFR][1000 genomes]
rs2871340	0.88[CEU][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.86[EUR][1000 genomes]
rs34529583	0.83[EUR][1000 genomes]
rs4331524	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4438499	0.88[CEU][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.84[EUR][1000 genomes]
rs4455176	0.83[EUR][1000 genomes]
rs4851267	1.00[YRI][hapmap]
rs4851292	0.88[CEU][hapmap]
rs4851293	0.87[CEU][hapmap]
rs6723909	0.88[CEU][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs7425449	0.88[CEU][hapmap]
rs7425797	0.88[CEU][hapmap]
rs7571306	0.85[EUR][1000 genomes]
rs764828	0.88[CEU][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs920269	0.88[CEU][hapmap]

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
rs4622752	LONRF2	cis	Skin Sun Exposed Lower leg	GTEx
rs4622752	LONRF2	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100879400-100896200	Weak transcription	Spleen	Spleen
2	chr2:100879400-100900200	Weak transcription	Brain Substantia Nigra	brain
3	chr2:100880200-100898400	Weak transcription	A549	lung
4	chr2:100884200-100900200	Weak transcription	Brain Angular Gyrus	brain
5	chr2:100884800-100897400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:100885600-100898200	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:100885600-100902000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:100887000-100900200	Weak transcription	Left Ventricle	heart
9	chr2:100887200-100898000	Weak transcription	Fetal Brain Female	brain
10	chr2:100887800-100895000	Weak transcription	K562	blood
11	chr2:100887800-100901800	Weak transcription	Fetal Intestine Small	intestine
12	chr2:100888000-100898000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:100888200-100896000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:100888400-100894600	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:100889400-100900200	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:100889600-100898200	Weak transcription	Fetal Brain Male	brain
17	chr2:100889600-100898400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:100890600-100892400	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr2:100890600-100900200	Weak transcription	Right Ventricle	heart
20	chr2:100891200-100892200	Strong transcription	Brain Anterior Caudate	brain
21	chr2:100891200-100892200	Strong transcription	Pancreas	Pancrea
22	chr2:100891200-100892200	Strong transcription	Skeletal Muscle Male	skeletal muscle
23	chr2:100891400-100892200	Strong transcription	Brain Germinal Matrix	brain
24	chr2:100891400-100892200	Strong transcription	Brain Inferior Temporal Lobe	brain
25	chr2:100891400-100900000	Weak transcription	Aorta	Aorta
26	chr2:100891600-100892200	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr2:100891600-100896000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr2:100891800-100892200	Enhancers	Fetal Muscle Trunk	muscle
29	chr2:100891800-100892400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr2:100891800-100900200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr2:100891800-100907600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr2:100892000-100894800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr2:100892000-100896200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr2:100892000-100896200	Weak transcription	Ovary	ovary
35	chr2:100892000-100898000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:100892000-100898600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:100892000-100902000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:100892000-100904000	Weak transcription	Gastric	stomach

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