Variant report

Variant	rs10799313
Chromosome Location	chr1:225662935-225662936
allele	C/G
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:39)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:225662398..225663268-chr1:226033119..226034385,8	K562	blood:
2	chr1:225625683..225626268-chr1:225662425..225662953,2	MCF-7	breast:
3	chr1:225660989..225663497-chr1:226070471..226072090,2	K562	blood:
4	chr1:225662379..225663286-chr1:226163400..226164300,7	K562	blood:
5	chr1:225602154..225602733-chr1:225662665..225663257,2	K562	blood:
6	chr1:225662357..225662998-chr1:225754575..225755137,2	K562	blood:
7	chr1:225662312..225663277-chr1:226032721..226034082,11	MCF-7	breast:
8	chr1:225662471..225663286-chr1:225959783..225960696,4	MCF-7	breast:
9	chr1:225662674..225663260-chr1:226156064..226156695,2	MCF-7	breast:
10	chr1:225662381..225663188-chr1:226098805..226099681,6	MCF-7	breast:
11	chr1:225661061..225665257-chr1:226163112..226166318,3	K562	blood:
12	chr1:225662588..225663159-chr1:225960250..225960988,2	MCF-7	breast:
13	chr1:225662383..225663164-chr1:225958651..225959497,2	MCF-7	breast:
14	chr1:225662353..225663278-chr1:226308878..226309804,6	K562	blood:
15	chr1:225662457..225663199-chr1:225705258..225705789,2	MCF-7	breast:
16	chr1:225662644..225663293-chr1:226308870..226309402,2	MCF-7	breast:
17	chr1:225662561..225663268-chr1:225685078..225685619,2	K562	blood:
18	chr1:225662349..225663258-chr1:225740687..225742425,6	K562	blood:
19	chr1:225662710..225663336-chr1:226154888..226155470,2	MCF-7	breast:
20	chr1:225662226..225663306-chr1:226163275..226164318,16	MCF-7	breast:
21	chr1:225662607..225663273-chr1:225994915..225995627,2	K562	blood:
22	chr1:225662226..225663837-chr1:226162713..226165257,2	K562	blood:
23	chr1:225662701..225663242-chr1:226175273..226175841,2	MCF-7	breast:
24	chr1:225662449..225663280-chr1:226160613..226161497,3	K562	blood:
25	chr1:225662402..225663343-chr1:226032820..226034152,12	MCF-7	breast:
26	chr1:225662537..225663284-chr1:225964788..225965783,3	K562	blood:
27	chr1:225662700..225663253-chr1:226040369..226040954,2	MCF-7	breast:
28	chr1:225661996..225663242-chr1:226163233..226164619,8	MCF-7	breast:
29	chr1:225662368..225663228-chr1:226027050..226027785,2	K562	blood:
30	chr1:225657432..225660259-chr1:225660834..225662970,2	K562	blood:
31	chr1:225662303..225663219-chr1:226174962..226175679,3	MCF-7	breast:
32	chr1:225662746..225665144-chr1:225672666..225674544,2	MCF-7	breast:
33	chr1:225662400..225663321-chr1:225843274..225843784,2	K562	blood:
34	chr1:225662577..225663310-chr1:226384412..226385341,3	K562	blood:
35	chr1:225662424..225663252-chr1:226071421..226072025,2	MCF-7	breast:
36	chr1:225662326..225663674-chr1:226098265..226099949,10	MCF-7	breast:
37	chr1:225615551..225616246-chr1:225662296..225663262,2	MCF-7	breast:
38	chr1:225662416..225663048-chr1:226150174..226150762,3	MCF-7	breast:
39	chr1:225662355..225663302-chr1:225959684..225960794,13	K562	blood:

No data

Variant related genes	Relation type
ENSG00000242861	Chromatin interaction
ENSG00000143815	Chromatin interaction
ENSG00000243709	Chromatin interaction
ENSG00000143742	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10753406	0.83[ASN][1000 genomes]
rs10799314	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10799315	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10799316	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10799317	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10799318	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10799319	0.83[ASN][1000 genomes]
rs10915830	0.80[ASN][1000 genomes]
rs10915833	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10915835	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915837	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10915838	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10915839	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11584675	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12028305	0.82[ASN][1000 genomes]
rs1222440	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12729655	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3820226	0.84[ASN][1000 genomes]
rs4653643	0.85[ASN][1000 genomes]
rs6426076	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6426077	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6426078	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668770	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6676201	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6678806	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6702555	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6751	0.86[ASN][1000 genomes]
rs7515907	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7515963	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7524766	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7541598	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7555139	0.82[ASN][1000 genomes]
rs7555553	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs947034	0.80[ASN][1000 genomes]
rs9804142	0.87[AFR][1000 genomes];0.84[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10799313	LBR	cis	Artery Tibial	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225655600-225677000	Weak transcription	Right Atrium	heart
2	chr1:225656800-225663000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:225660600-225666200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:225660800-225663400	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr1:225660800-225666200	Enhancers	Primary T cells fromperipheralblood	blood
6	chr1:225660800-225666200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr1:225660800-225666800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:225661000-225663200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:225661000-225663200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:225661000-225666200	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr1:225661000-225666200	Enhancers	Fetal Thymus	thymus
12	chr1:225661200-225663400	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr1:225661600-225663800	Weak transcription	Primary T cells from cord blood	blood
14	chr1:225661800-225663200	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr1:225662000-225663000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:225662000-225663200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr1:225662000-225663400	Enhancers	Gastric	stomach
18	chr1:225662000-225663400	Enhancers	Lung	lung
19	chr1:225662000-225667000	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr1:225662200-225663000	Weak transcription	Right Ventricle	heart
21	chr1:225662200-225671800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:225662400-225663000	Enhancers	K562	blood
23	chr1:225662400-225663000	Enhancers	NHLF	lung
24	chr1:225662400-225663200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr1:225662400-225663200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:225662400-225663200	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr1:225662400-225663200	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr1:225662400-225663200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:225662400-225663200	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr1:225662400-225663200	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr1:225662400-225663200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:225662400-225663200	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr1:225662400-225663200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:225662400-225663200	Enhancers	Fetal Heart	heart
35	chr1:225662400-225663200	Enhancers	Fetal Intestine Large	intestine
36	chr1:225662400-225663200	Enhancers	Fetal Muscle Leg	muscle
37	chr1:225662400-225663200	Enhancers	Fetal Stomach	stomach
38	chr1:225662400-225663200	Enhancers	Stomach Mucosa	stomach
39	chr1:225662400-225663200	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr1:225662400-225663200	Enhancers	Spleen	Spleen
41	chr1:225662400-225663200	Enhancers	HSMMtube	muscle
42	chr1:225662400-225663200	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr1:225662400-225663200	Enhancers	NH-A	brain
44	chr1:225662400-225663400	Enhancers	Primary B cells from cord blood	blood
45	chr1:225662400-225663400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:225662400-225663400	Enhancers	Esophagus	oesophagus
47	chr1:225662400-225663400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr1:225662400-225663400	Enhancers	Fetal Brain Male	brain
49	chr1:225662400-225663400	Enhancers	Fetal Intestine Small	intestine
50	chr1:225662400-225663400	Enhancers	Fetal Muscle Trunk	muscle

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