Variant report

Variant	rs6541081
Chromosome Location	chr1:10253524-10253525
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11510094	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11801734	1.00[ASN][1000 genomes]
rs11802484	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11812055	1.00[ASN][1000 genomes]
rs11812074	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61784567	1.00[ASN][1000 genomes]
rs6541082	1.00[ASN][1000 genomes]
rs6691645	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[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	nsv527217	chr1:10093457-10257167	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6541081	LZIC	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10233200-10258200	Weak transcription	Hela-S3	cervix
2	chr1:10236400-10258200	Weak transcription	HSMM	muscle
3	chr1:10240000-10255400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:10241000-10254000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:10241000-10254200	Weak transcription	Brain Anterior Caudate	brain
6	chr1:10241000-10254200	Weak transcription	Brain Hippocampus Middle	brain
7	chr1:10241000-10254200	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:10241000-10254600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:10241000-10255600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:10241000-10257200	Weak transcription	Ovary	ovary
11	chr1:10241000-10258000	Weak transcription	Psoas Muscle	Psoas
12	chr1:10241200-10254000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:10241200-10254200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:10241200-10254200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:10241200-10259000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:10241400-10255600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:10241600-10254000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:10241600-10254000	Weak transcription	Osteobl	bone
19	chr1:10241800-10254000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:10244200-10256800	Weak transcription	Fetal Stomach	stomach
21	chr1:10247200-10254200	Weak transcription	Fetal Kidney	kidney
22	chr1:10247200-10255400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:10250000-10261000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr1:10250000-10269800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:10252200-10253600	Enhancers	HepG2	liver
26	chr1:10252800-10254200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:10253400-10253600	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr1:10253400-10253800	Enhancers	Fetal Muscle Leg	muscle
29	chr1:10253400-10253800	Enhancers	Placenta	Placenta

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