Variant report

Variant	rs315538
Chromosome Location	chr1:84818224-84818225
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1067072	0.99[ASN][1000 genomes]
rs1246546	0.90[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs1246549	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1246550	0.90[CHB][hapmap];0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs160612	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1690702	1.00[CHB][hapmap];0.86[JPT][hapmap];0.99[ASN][1000 genomes]
rs1699157	0.91[ASN][1000 genomes]
rs170278	1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs172735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17536473	1.00[CEU][hapmap]
rs178367	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs178368	1.00[ASN][1000 genomes]
rs186405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2055115	1.00[CEU][hapmap]
rs315520	1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs315521	1.00[ASN][1000 genomes]
rs315522	1.00[ASN][1000 genomes]
rs315523	1.00[ASN][1000 genomes]
rs315524	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs315525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs315526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs315527	1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs315528	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs315530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs315531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs315532	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs315533	0.92[ASN][1000 genomes]
rs315535	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs315536	1.00[ASN][1000 genomes]
rs315539	0.92[ASN][1000 genomes]
rs315540	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs315546	1.00[ASN][1000 genomes]
rs315547	0.93[ASN][1000 genomes]
rs315548	1.00[ASN][1000 genomes]
rs315549	1.00[ASN][1000 genomes]
rs315552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs315553	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs315554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs315555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs315556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs316660	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs316661	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs316662	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs316663	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs316664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs316665	0.99[ASN][1000 genomes]
rs511087	1.00[ASN][1000 genomes]
rs592464	0.99[ASN][1000 genomes]
rs786653	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830414	chr1:84636738-84824651	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv830426	chr1:84704924-84856229	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84795800-84827000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:84810200-84819800	Weak transcription	HSMM	muscle
3	chr1:84814000-84818600	Weak transcription	NHLF	lung
4	chr1:84814000-84819400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:84814200-84828800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:84814200-84831400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:84814600-84825600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:84815000-84819200	Enhancers	Brain Substantia Nigra	brain
9	chr1:84815200-84820000	Enhancers	Brain Anterior Caudate	brain
10	chr1:84816600-84821000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr1:84817000-84820000	Enhancers	Brain Cingulate Gyrus	brain
12	chr1:84817000-84820000	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr1:84817400-84818800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:84817600-84818800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:84817600-84826200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:84817800-84820200	Enhancers	Brain Hippocampus Middle	brain
17	chr1:84818000-84818400	Enhancers	NH-A	brain
18	chr1:84818000-84818600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:84818000-84820200	Enhancers	Fetal Stomach	stomach
20	chr1:84818000-84820400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:84818000-84820400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:84818000-84820400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:84818200-84819000	Enhancers	Brain Angular Gyrus	brain
24	chr1:84818200-84819000	Enhancers	HMEC	breast
25	chr1:84818200-84819800	Enhancers	Muscle Satellite Cultured Cells	--
26	chr1:84818200-84820000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:84818200-84820000	Enhancers	NHDF-Ad	bronchial
28	chr1:84818200-84820000	Enhancers	Osteobl	bone
29	chr1:84818200-84820200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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