Variant report

Variant	rs10449249
Chromosome Location	chr1:225662122-225662123
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225660989..225663497-chr1:226070471..226072090,2	K562	blood:
2	chr1:225661061..225665257-chr1:226163112..226166318,3	K562	blood:
3	chr1:225660270..225662835-chr1:225667398..225670221,2	MCF-7	breast:
4	chr1:225661996..225663242-chr1:226163233..226164619,8	MCF-7	breast:
5	chr1:225657432..225660259-chr1:225660834..225662970,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10915829	0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11377355	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12022013	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12026034	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12031651	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12037289	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12038373	0.89[EUR][1000 genomes]
rs12042273	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12042698	0.80[ASN][1000 genomes]
rs12239415	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1340866	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1340870	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1340871	0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1340872	0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16845000	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2184778	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2185531	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2296880	0.81[EUR][1000 genomes]
rs28620013	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3766931	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3795443	0.84[ASN][1000 genomes]
rs4129816	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55751087	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs56169721	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58269599	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59912270	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61333083	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674621	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6681559	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6684314	0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6684956	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6694938	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74146931	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs74146994	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs74149835	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74149844	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7415548	0.89[EUR][1000 genomes]
rs7543444	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1004851	chr1:225614140-225684184	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv34905	chr1:225631404-225676582	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv873227	chr1:225656388-225687981	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv8880	chr1:225656408-225687710	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv826842	chr1:225658062-225686586	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv441740	chr1:225659217-225684196	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10449249	LBR	cis	Artery Tibial	GTEx
rs10449249	LBR	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225649800-225662600	Weak transcription	Pancreas	Pancrea
2	chr1:225651400-225662400	Weak transcription	Fetal Brain Male	brain
3	chr1:225653600-225662400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:225653600-225662400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:225655400-225662400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:225655600-225677000	Weak transcription	Right Atrium	heart
7	chr1:225656400-225662400	Weak transcription	Liver	Liver
8	chr1:225656400-225662600	Weak transcription	Thymus	Thymus
9	chr1:225656600-225662600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:225656800-225662400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr1:225656800-225662800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:225656800-225663000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:225657000-225662400	Weak transcription	Primary B cells from cord blood	blood
14	chr1:225657000-225662400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:225657200-225662400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr1:225657600-225662400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:225658800-225662400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:225660000-225662400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:225660400-225662400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:225660600-225666200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:225660800-225662800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr1:225660800-225663400	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr1:225660800-225666200	Enhancers	Primary T cells fromperipheralblood	blood
24	chr1:225660800-225666200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr1:225660800-225666800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:225661000-225662400	Enhancers	Stomach Smooth Muscle	stomach
27	chr1:225661000-225663200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:225661000-225663200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:225661000-225666200	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr1:225661000-225666200	Enhancers	Fetal Thymus	thymus
31	chr1:225661200-225662400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:225661200-225662800	Enhancers	Brain Cingulate Gyrus	brain
33	chr1:225661200-225663400	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr1:225661400-225662400	Weak transcription	Brain Hippocampus Middle	brain
35	chr1:225661400-225662800	Enhancers	Brain Substantia Nigra	brain
36	chr1:225661600-225662200	Weak transcription	Brain Angular Gyrus	brain
37	chr1:225661600-225663800	Weak transcription	Primary T cells from cord blood	blood
38	chr1:225661800-225662800	Enhancers	Rectal Smooth Muscle	rectum
39	chr1:225661800-225663200	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr1:225662000-225662200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:225662000-225662200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:225662000-225662200	Enhancers	Right Ventricle	heart
43	chr1:225662000-225662400	Flanking Active TSS	Colon Smooth Muscle	Colon
44	chr1:225662000-225662400	Weak transcription	Spleen	Spleen
45	chr1:225662000-225662600	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr1:225662000-225663000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:225662000-225663200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr1:225662000-225663400	Enhancers	Gastric	stomach
49	chr1:225662000-225663400	Enhancers	Lung	lung
50	chr1:225662000-225667000	Enhancers	Primary T killer memory cells from peripheral blood	blood

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