Variant report

Variant	rs6426077
Chromosome Location	chr1:225659815-225659816
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225657432..225660259-chr1:225660834..225662970,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC092811.1-1	chr1:225659565-225660157	XLOC_000585

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10753406	0.88[ASN][1000 genomes]
rs10799311	0.82[ASN][1000 genomes]
rs10799313	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10799315	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10799316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10799317	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10799318	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10799319	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs10915828	0.93[CHB][hapmap];0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs10915830	0.85[ASN][1000 genomes]
rs10915833	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10915835	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10915837	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10915838	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10915839	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10915847	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs11584675	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1222440	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12729655	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2639703	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap]
rs2657569	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs2840967	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap]
rs2840968	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap]
rs3820226	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs4653639	0.84[ASN][1000 genomes]
rs4653643	0.85[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap];0.89[TSI][hapmap];0.81[ASN][1000 genomes]
rs487591	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap]
rs498350	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs554744	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs554992	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs576861	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap]
rs6426076	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6426078	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6668770	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6676201	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6678806	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6697783	0.93[CHB][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap]
rs6702555	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6751	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.81[ASN][1000 genomes]
rs712062	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap]
rs7515907	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7515963	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7524766	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7541598	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7555553	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs947034	0.85[ASN][1000 genomes]
rs9804142	0.85[AFR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6426077	LBR	cis	Artery Tibial	GTEx

Chromatin state (count:42 , 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	chr1:225655800-225661200	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:225655800-225661800	Weak transcription	Spleen	Spleen
9	chr1:225655800-225662000	Weak transcription	Right Ventricle	heart
10	chr1:225656400-225660000	Enhancers	Fetal Thymus	thymus
11	chr1:225656400-225662400	Weak transcription	Liver	Liver
12	chr1:225656400-225662600	Weak transcription	Thymus	Thymus
13	chr1:225656600-225661800	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr1:225656600-225662000	Weak transcription	Lung	lung
15	chr1:225656600-225662600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:225656800-225661000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:225656800-225662400	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr1:225656800-225662800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:225656800-225663000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:225657000-225661200	Weak transcription	Primary T cells from cord blood	blood
21	chr1:225657000-225662000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:225657000-225662400	Weak transcription	Primary B cells from cord blood	blood
23	chr1:225657000-225662400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:225657200-225660800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr1:225657200-225660800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:225657200-225661000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:225657200-225661000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:225657200-225661200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr1:225657200-225662400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr1:225657400-225660800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr1:225657400-225660800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:225657400-225660800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr1:225657400-225662000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr1:225657600-225662400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr1:225658600-225660000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:225658800-225662400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:225659000-225660800	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:225659000-225661800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr1:225659600-225660000	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr1:225659600-225660200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:225659600-225662000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:225659800-225661000	Weak transcription	Stomach Smooth Muscle	stomach

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