Variant report

Variant	rs6681559
Chromosome Location	chr1:225648156-225648157
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225626720..225628379-chr1:225647904..225650755,2	K562	blood:
2	chr1:225637801..225642696-chr1:225647950..225650939,4	K562	blood:
3	chr1:225646024..225648970-chr1:225656905..225658780,2	K562	blood:
4	chr1:225632782..225636036-chr1:225646050..225649453,3	K562	blood:
5	chr1:225646305..225648757-chr1:225649524..225652760,3	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10449249	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10915829	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11377355	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12022013	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12026034	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12031651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12037289	0.87[ASN][1000 genomes]
rs12042273	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12239415	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12405879	0.84[ASN][1000 genomes]
rs12405904	0.84[ASN][1000 genomes]
rs1340866	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1340870	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1340871	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1340872	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16845000	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2184778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2185531	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2297747	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28620013	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3795443	1.00[CHB][hapmap]
rs4129816	0.85[ASN][1000 genomes]
rs55751087	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56169721	0.87[ASN][1000 genomes]
rs58269599	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59912270	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61333083	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6674621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6684314	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684956	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6694938	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74146931	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74146994	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74149835	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs74149844	0.87[ASN][1000 genomes]
rs7543444	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[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
rs6681559	LBR	cis	Esophagus Muscularis	GTEx
rs6681559	LBR	cis	Artery Tibial	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225634600-225648400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:225636200-225650000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:225637800-225648400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:225642400-225650800	Weak transcription	Right Atrium	heart
5	chr1:225642400-225653000	Weak transcription	Primary B cells from cord blood	blood
6	chr1:225642400-225655200	Weak transcription	Small Intestine	intestine
7	chr1:225642600-225655000	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:225642800-225648800	Weak transcription	Pancreas	Pancrea
9	chr1:225642800-225650000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:225642800-225652800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:225643000-225648400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:225643000-225648400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:225643000-225648600	Weak transcription	Stomach Mucosa	stomach
14	chr1:225643000-225650400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:225643000-225651000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:225645800-225648200	Enhancers	Hela-S3	cervix
17	chr1:225645800-225648800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:225645800-225648800	Enhancers	NH-A	brain
19	chr1:225645800-225648800	Enhancers	Osteobl	bone
20	chr1:225645800-225649400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:225646400-225648800	Weak transcription	Fetal Heart	heart
22	chr1:225646400-225653600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:225647000-225648800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:225647000-225649000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:225647000-225649000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:225647000-225649000	Enhancers	NHDF-Ad	bronchial
27	chr1:225647000-225649000	Enhancers	NHLF	lung
28	chr1:225647000-225649200	Enhancers	NHEK	skin
29	chr1:225647000-225649400	Enhancers	Muscle Satellite Cultured Cells	--
30	chr1:225647000-225649400	Enhancers	HSMM	muscle
31	chr1:225647000-225651600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr1:225647000-225651600	Enhancers	Fetal Muscle Leg	muscle
33	chr1:225647000-225653600	Enhancers	Esophagus	oesophagus
34	chr1:225647000-225654600	Enhancers	Fetal Thymus	thymus
35	chr1:225647000-225654800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:225647200-225649600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:225647200-225649800	Enhancers	Thymus	Thymus
38	chr1:225647200-225651600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr1:225647400-225648400	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr1:225647400-225651200	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr1:225647400-225654800	Enhancers	Primary T cells fromperipheralblood	blood
42	chr1:225647600-225648400	Weak transcription	Adipose Nuclei	Adipose
43	chr1:225647600-225648800	Enhancers	HMEC	breast
44	chr1:225647600-225649000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:225647600-225649200	Enhancers	Fetal Muscle Trunk	muscle
46	chr1:225647600-225649400	Enhancers	Dnd41	blood
47	chr1:225647600-225649600	Enhancers	Duodenum Mucosa	Duodenum
48	chr1:225647600-225650200	Enhancers	Spleen	Spleen
49	chr1:225647600-225650200	Enhancers	A549	lung
50	chr1:225647600-225652000	Enhancers	Fetal Stomach	stomach

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