Variant report

Variant	rs10915829
Chromosome Location	chr1:225641541-225641542
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225613325..225614871-chr1:225640956..225643217,2	K562	blood:
2	chr1:225637801..225642696-chr1:225647950..225650939,4	K562	blood:
3	chr1:225640956..225643157-chr1:226491999..226493794,2	K562	blood:
4	chr1:225633065..225638606-chr1:225639136..225643843,7	MCF-7	breast:
5	chr1:225636376..225639030-chr1:225641511..225643648,3	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10449249	0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11377355	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12022013	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12026034	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12031651	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12037289	0.87[ASN][1000 genomes]
rs12038373	0.89[CHD][hapmap];0.82[MEX][hapmap]
rs12042273	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12239415	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12405879	0.84[ASN][1000 genomes]
rs12405904	0.84[ASN][1000 genomes]
rs1340866	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1340870	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1340871	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1340872	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16845000	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2184778	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2185531	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2297747	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28620013	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766931	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3795443	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs4129816	0.85[ASN][1000 genomes]
rs487591	0.82[YRI][hapmap]
rs55751087	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56169721	0.87[ASN][1000 genomes]
rs58269599	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59912270	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61333083	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6674621	1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs6681559	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684314	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684956	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6694938	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74146931	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74146994	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74149835	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs74149844	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7539651	0.88[GIH][hapmap];0.84[TSI][hapmap]
rs7543444	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10915829	LBR	cis	Artery Tibial	GTEx
rs10915829	LBR	cis	Esophagus Muscularis	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225633600-225642000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:225634200-225642000	Weak transcription	K562	blood
3	chr1:225634600-225648400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:225635000-225647800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:225635400-225641800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr1:225635600-225641600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:225635600-225642000	Weak transcription	Pancreas	Pancrea
8	chr1:225636200-225650000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:225636400-225641600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:225636400-225641600	Weak transcription	NHLF	lung
11	chr1:225636400-225642000	Weak transcription	Right Atrium	heart
12	chr1:225636600-225641600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:225636600-225641800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:225636600-225642000	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:225637200-225641600	Weak transcription	Osteobl	bone
16	chr1:225637600-225641800	Weak transcription	Small Intestine	intestine
17	chr1:225637800-225642000	Weak transcription	Gastric	stomach
18	chr1:225637800-225642000	Weak transcription	Lung	lung
19	chr1:225637800-225647600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr1:225637800-225648400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:225638800-225642000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:225638800-225642000	Weak transcription	HUVEC	blood vessel
23	chr1:225638800-225642200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:225639000-225642200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:225639200-225641600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:225639200-225641800	Weak transcription	HSMMtube	muscle
27	chr1:225639400-225641600	Weak transcription	NHEK	skin
28	chr1:225639400-225647000	Weak transcription	Esophagus	oesophagus
29	chr1:225639400-225648000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:225639600-225641800	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr1:225639600-225642000	Weak transcription	NH-A	brain
32	chr1:225639800-225641600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:225639800-225641600	Weak transcription	HMEC	breast
34	chr1:225640000-225643000	Enhancers	Rectal Smooth Muscle	rectum
35	chr1:225640200-225641800	Weak transcription	Fetal Thymus	thymus
36	chr1:225640200-225642000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:225640200-225642200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:225640400-225642000	Weak transcription	Fetal Stomach	stomach
39	chr1:225641000-225642000	Enhancers	Stomach Smooth Muscle	stomach
40	chr1:225641200-225642600	Enhancers	Thymus	Thymus
41	chr1:225641200-225643000	Enhancers	Liver	Liver
42	chr1:225641200-225643000	Enhancers	HepG2	liver
43	chr1:225641400-225641600	Enhancers	A549	lung
44	chr1:225641400-225641800	Flanking Active TSS	Colon Smooth Muscle	Colon
45	chr1:225641400-225642000	Enhancers	Hela-S3	cervix
46	chr1:225641400-225642800	Enhancers	HSMM	muscle
47	chr1:225641400-225643000	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr1:225641400-225643000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:225641400-225643000	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr1:225641400-225643000	Enhancers	Stomach Mucosa	stomach

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