Variant report

Variant	rs10799314
Chromosome Location	chr1:225666518-225666519
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225652545..225654089-chr1:225665937..225667726,2	K562	blood:
2	chr1:225664480..225667161-chr1:225903900..225905865,2	K562	blood:
3	chr1:225665630..225667137-chr1:226308801..226311216,2	K562	blood:

Variant related genes	Relation type
ENSG00000234476	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10753406	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10799311	0.89[AMR][1000 genomes]
rs10799313	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10799315	0.88[AFR][1000 genomes]
rs10799316	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10799317	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10799318	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10799319	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10915830	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10915833	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10915834	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10915835	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10915837	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10915838	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10915839	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10915847	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11584675	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12028305	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1222440	0.84[ASN][1000 genomes]
rs12729655	0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3820226	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3856156	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4653639	0.83[AMR][1000 genomes]
rs4653643	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs487591	0.82[ASN][1000 genomes]
rs498350	0.82[ASN][1000 genomes]
rs510293	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs511649	0.82[ASN][1000 genomes]
rs516249	0.82[ASN][1000 genomes]
rs551996	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs554744	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs554992	0.82[ASN][1000 genomes]
rs561656	0.82[ASN][1000 genomes]
rs576861	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6426076	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6426078	0.84[ASN][1000 genomes]
rs6668770	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6676201	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6678806	0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6702555	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6751	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs712062	0.82[ASN][1000 genomes]
rs7515907	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7515963	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7524766	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7540181	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7541598	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7555139	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7555553	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs947034	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9804142	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
8	nsv433350	chr1:225665284-225686025	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv873228	chr1:225665284-225687981	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
10	esv2753202	chr1:225665694-225676571	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	n/a
11	esv2756886	chr1:225665694-225703485	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
12	esv2759003	chr1:225665694-225703485	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10799314	LBR	cis	Artery Tibial	GTEx
rs10799314	RP11-496N12.9	cis	Thyroid	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225655600-225677000	Weak transcription	Right Atrium	heart
2	chr1:225660800-225666800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:225662000-225667000	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr1:225662200-225671800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:225662600-225671800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:225663200-225668600	Weak transcription	Fetal Intestine Large	intestine
7	chr1:225663200-225668600	Weak transcription	Pancreas	Pancrea
8	chr1:225663200-225668600	Weak transcription	Stomach Mucosa	stomach
9	chr1:225663200-225668800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:225663200-225668800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:225663200-225669800	Weak transcription	Ovary	ovary
12	chr1:225663200-225670200	Weak transcription	Osteobl	bone
13	chr1:225663200-225683800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:225663200-225686400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:225663200-225696400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr1:225663400-225667400	Weak transcription	Fetal Brain Male	brain
17	chr1:225663400-225668400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr1:225663400-225668800	Weak transcription	Brain Germinal Matrix	brain
19	chr1:225663400-225668800	Weak transcription	Fetal Brain Female	brain
20	chr1:225663400-225668800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:225663400-225669000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:225663400-225669600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:225663400-225686000	Weak transcription	A549	lung
24	chr1:225664000-225667200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:225664000-225670000	Enhancers	Primary B cells from peripheral blood	blood
26	chr1:225665200-225670400	Enhancers	Primary B cells from cord blood	blood
27	chr1:225665600-225667400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr1:225665800-225667000	Weak transcription	NHEK	skin
29	chr1:225665800-225667200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:225665800-225668400	Weak transcription	Placenta	Placenta
31	chr1:225665800-225668800	Weak transcription	Colon Smooth Muscle	Colon
32	chr1:225666000-225668000	Weak transcription	Spleen	Spleen
33	chr1:225666000-225668600	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr1:225666000-225669800	Weak transcription	Brain Anterior Caudate	brain
35	chr1:225666000-225696800	Weak transcription	Esophagus	oesophagus
36	chr1:225666200-225666600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:225666200-225668000	Weak transcription	GM12878-XiMat	blood
38	chr1:225666200-225668600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr1:225666200-225668600	Weak transcription	Fetal Thymus	thymus
40	chr1:225666400-225666800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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