Variant report

Variant	rs10799317
Chromosome Location	chr1:225670738-225670739
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225667455..225673405-chr1:225674170..225678275,6	MCF-7	breast:
2	chr1:225668772..225671386-chr1:225671515..225673412,2	K562	blood:
3	chr1:225668756..225671445-chr1:225674981..225676551,3	K562	blood:

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10753406	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10799311	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10799313	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10799314	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10799315	0.81[AFR][1000 genomes]
rs10799316	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10799318	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10799319	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10915828	0.83[ASN][1000 genomes]
rs10915830	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10915833	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10915834	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10915835	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10915837	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10915838	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10915839	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915847	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11584675	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12028305	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1222440	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12729655	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2639703	0.82[EUR][1000 genomes]
rs2639716	0.81[EUR][1000 genomes]
rs2657564	0.82[EUR][1000 genomes]
rs2657569	0.81[EUR][1000 genomes]
rs2840958	0.83[EUR][1000 genomes]
rs2840967	0.81[EUR][1000 genomes]
rs2840968	0.81[EUR][1000 genomes]
rs3820226	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856156	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4653639	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4653643	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs476540	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs487591	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs498350	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs510293	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs511649	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs516249	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs551996	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs554744	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs554992	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs561656	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs576861	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6426076	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6426077	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6426078	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6668770	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6676201	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6678806	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6702555	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6751	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs712062	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7515907	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7515963	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7524766	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7540181	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7541598	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7555139	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7555553	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs812523	0.83[ASN][1000 genomes]
rs947034	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9804142	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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
13	nsv873229	chr1:225668031-225685928	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
14	nsv873230	chr1:225668524-225687981	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10799317	RP11-496N12.9	cis	Thyroid	GTEx
rs10799317	LBR	cis	Artery Tibial	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225655600-225677000	Weak transcription	Right Atrium	heart
2	chr1:225662200-225671800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:225662600-225671800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:225663200-225683800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:225663200-225686400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:225663200-225696400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:225663400-225686000	Weak transcription	A549	lung
8	chr1:225666000-225696800	Weak transcription	Esophagus	oesophagus
9	chr1:225667400-225684400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:225668400-225670800	Enhancers	Duodenum Mucosa	Duodenum
11	chr1:225668800-225670800	Enhancers	Fetal Lung	lung
12	chr1:225668800-225672200	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr1:225668800-225672400	Enhancers	Colon Smooth Muscle	Colon
14	chr1:225669000-225672200	Weak transcription	Fetal Thymus	thymus
15	chr1:225669000-225687800	Weak transcription	Placenta	Placenta
16	chr1:225669200-225671800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:225669200-225673600	Enhancers	Fetal Muscle Leg	muscle
18	chr1:225669600-225670800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:225669600-225670800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
20	chr1:225669600-225670800	Enhancers	Brain Hippocampus Middle	brain
21	chr1:225669600-225671000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:225669600-225672400	Enhancers	Rectal Smooth Muscle	rectum
23	chr1:225669800-225670800	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr1:225669800-225670800	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr1:225669800-225670800	Enhancers	Ovary	ovary
26	chr1:225669800-225671800	Enhancers	Fetal Stomach	stomach
27	chr1:225669800-225673400	Enhancers	Fetal Brain Male	brain
28	chr1:225669800-225696800	Weak transcription	Pancreas	Pancrea
29	chr1:225670000-225670800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:225670000-225670800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:225670000-225670800	Enhancers	HSMMtube	muscle
32	chr1:225670200-225670800	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr1:225670200-225670800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr1:225670200-225670800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:225670200-225670800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:225670200-225670800	Enhancers	Aorta	Aorta
37	chr1:225670200-225670800	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr1:225670200-225670800	Enhancers	NH-A	brain
39	chr1:225670200-225671000	Enhancers	Osteobl	bone
40	chr1:225670400-225670800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:225670400-225670800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:225670400-225670800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr1:225670400-225670800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:225670400-225670800	Enhancers	Brain Angular Gyrus	brain
45	chr1:225670400-225670800	Enhancers	NHDF-Ad	bronchial
46	chr1:225670400-225670800	Bivalent Enhancer	NHLF	lung
47	chr1:225670400-225672000	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr1:225670400-225672200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:225670600-225670800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:225670600-225670800	Enhancers	H9 Cell Line	embryonic stem cell

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