Variant report

Variant	rs764828
Chromosome Location	chr2:100908634-100908635
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:29)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:100908542..100909110-chr2:100937511..100938311,3	MCF-7	breast:
2	chr2:99952367..99954549-chr2:100906895..100909428,2	K562	blood:
3	chr2:100907987..100912107-chr2:100920120..100922978,3	MCF-7	breast:
4	chr2:100907128..100908845-chr2:101037649..101040314,2	MCF-7	breast:
5	chr2:100887822..100891668-chr2:100905183..100909067,4	MCF-7	breast:
6	chr2:100882860..100889379-chr2:100906197..100910186,11	MCF-7	breast:
7	chr2:100884322..100884994-chr2:100908557..100909198,2	MCF-7	breast:
8	chr2:100887980..100890347-chr2:100906577..100908691,2	K562	blood:
9	chr2:100907864..100908724-chr2:100937511..100938051,2	MCF-7	breast:
10	chr2:100906831..100909358-chr2:100926038..100929328,3	MCF-7	breast:
11	chr2:100889401..100893026-chr2:100904259..100909793,5	MCF-7	breast:
12	chr2:100900693..100917248-chr2:100932005..100942326,51	MCF-7	breast:
13	chr2:100906911..100909075-chr2:101026496..101029080,2	MCF-7	breast:
14	chr2:100908492..100909141-chr2:100938432..100939141,2	MCF-7	breast:
15	chr2:100895478..100897134-chr2:100908252..100910044,2	K562	blood:
16	chr2:100907851..100910506-chr2:101025959..101028918,2	MCF-7	breast:
17	chr2:100878643..100880888-chr2:100907492..100909514,2	K562	blood:
18	chr2:100879379..100882180-chr2:100906907..100909582,4	MCF-7	breast:
19	chr2:100906645..100910351-chr2:100915314..100919031,3	K562	blood:
20	chr2:100908539..100910145-chr2:100995455..100997648,2	MCF-7	breast:
21	chr2:100888847..100890677-chr2:100907191..100910178,2	K562	blood:
22	chr2:100907126..100910810-chr2:100936315..100940527,7	K562	blood:
23	chr2:100908367..100909141-chr2:100938432..100939300,4	MCF-7	breast:
24	chr2:100906230..100908790-chr2:100951574..100954485,3	MCF-7	breast:
25	chr2:100875966..100878799-chr2:100906876..100908974,2	MCF-7	breast:
26	chr2:100891457..100894388-chr2:100906302..100910364,4	K562	blood:
27	chr2:100906194..100910090-chr2:100935878..100940937,6	K562	blood:
28	chr2:100893081..100895089-chr2:100906389..100909363,2	MCF-7	breast:
29	chr2:100908082..100908744-chr2:100938685..100939223,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000158417	Chromatin interaction
ENSG00000170500	Chromatin interaction
ENSG00000115514	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10176062	0.83[JPT][hapmap]
rs10180423	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs10195018	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs10195793	0.80[EUR][1000 genomes]
rs10201565	0.81[ASN][1000 genomes]
rs11123822	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123823	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]
rs11123824	0.81[EUR][1000 genomes]
rs11123826	0.81[CEU][hapmap]
rs11682748	0.92[CEU][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs11686293	0.81[EUR][1000 genomes]
rs11689439	0.81[EUR][1000 genomes]
rs11691684	0.82[EUR][1000 genomes]
rs11693044	0.81[EUR][1000 genomes]
rs11693424	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs11694723	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs11890655	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs11902303	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs12612755	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12615466	0.81[EUR][1000 genomes]
rs12622318	0.81[EUR][1000 genomes]
rs12712075	0.80[EUR][1000 genomes]
rs12999779	0.81[EUR][1000 genomes]
rs13001423	0.81[EUR][1000 genomes]
rs13006224	0.82[EUR][1000 genomes]
rs13019179	0.84[EUR][1000 genomes]
rs13020451	0.81[EUR][1000 genomes]
rs13023534	0.80[EUR][1000 genomes]
rs13391517	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs13400045	0.80[ASN][1000 genomes]
rs13409545	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs1530028	0.92[CEU][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs17023901	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs1866198	0.81[EUR][1000 genomes]
rs1967339	0.82[EUR][1000 genomes]
rs1967341	0.80[EUR][1000 genomes]
rs2067783	0.85[CEU][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap]
rs2871340	0.82[JPT][hapmap]
rs4264577	0.81[CEU][hapmap]
rs4438499	0.82[JPT][hapmap]
rs4622752	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]
rs4850925	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4851288	0.81[CEU][hapmap]
rs4851292	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs4851293	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs55759234	0.85[ASN][1000 genomes]
rs6723909	0.82[JPT][hapmap]
rs7425449	0.92[CEU][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs7425797	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7556910	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs7571306	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs920269	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs920270	0.80[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
rs764828	LONRF2	cis	Skin Sun Exposed Lower leg	GTEx
rs764828	LONRF2	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100892200-100909800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr2:100898400-100915600	Weak transcription	Right Atrium	heart
3	chr2:100898800-100915000	Weak transcription	Adipose Nuclei	Adipose
4	chr2:100900200-100919000	Strong transcription	Fetal Brain Female	brain
5	chr2:100900800-100926600	Weak transcription	Right Ventricle	heart
6	chr2:100901000-100937000	Weak transcription	Fetal Brain Male	brain
7	chr2:100903200-100918000	Weak transcription	Liver	Liver
8	chr2:100903400-100909400	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:100903400-100930800	Weak transcription	Brain Substantia Nigra	brain
10	chr2:100903600-100914400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:100903600-100926200	Weak transcription	Fetal Kidney	kidney
12	chr2:100906400-100909200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:100906600-100911400	Strong transcription	Brain Germinal Matrix	brain
14	chr2:100906800-100909000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:100906800-100909000	Enhancers	Fetal Thymus	thymus
16	chr2:100906800-100909200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:100906800-100910000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr2:100906800-100910600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:100906800-100910600	Enhancers	Placenta	Placenta
20	chr2:100907000-100908800	Enhancers	Pancreas	Pancrea
21	chr2:100907000-100909000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:100907000-100909000	Enhancers	Ovary	ovary
23	chr2:100907000-100909000	Enhancers	Stomach Mucosa	stomach
24	chr2:100907000-100909200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:100907000-100909200	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr2:100907000-100909400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr2:100907000-100909600	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr2:100907000-100909800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr2:100907000-100909800	Enhancers	Osteobl	bone
30	chr2:100907000-100910000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:100907000-100912000	Weak transcription	Aorta	Aorta
32	chr2:100907200-100909000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:100907200-100909000	Enhancers	Fetal Intestine Large	intestine
34	chr2:100907200-100909000	Enhancers	Fetal Intestine Small	intestine
35	chr2:100907200-100909200	Enhancers	HMEC	breast
36	chr2:100907200-100909400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:100907200-100909400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr2:100907200-100909600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:100907200-100909800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:100907200-100909800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr2:100907400-100908800	Flanking Active TSS	K562	blood
42	chr2:100907400-100909000	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr2:100907400-100909000	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr2:100907400-100909000	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr2:100907400-100909000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:100907400-100909000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:100907400-100909000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr2:100907400-100909000	Enhancers	Colon Smooth Muscle	Colon
49	chr2:100907600-100908800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:100907600-100908800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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