Variant report

Variant	rs6540619
Chromosome Location	chr1:210862656-210862657
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1934618	0.81[CEU][hapmap];0.86[CHB][hapmap];0.84[YRI][hapmap]
rs2226022	0.91[EUR][1000 genomes]
rs2226023	1.00[CEU][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs3135473	0.84[YRI][hapmap]
rs4951542	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4951765	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6540620	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7554097	0.96[CEU][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873148	chr1:210665583-210994339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv873150	chr1:210808270-210893233	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv468083	chr1:210854815-210876192	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv549123	chr1:210854815-210876192	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6540619	CDK18	cis	parietal	SCAN
rs6540619	C1orf107	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210835400-210863200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:210838000-210880400	Weak transcription	Gastric	stomach
3	chr1:210845400-210866000	Weak transcription	Spleen	Spleen
4	chr1:210846000-210865600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:210846200-210865800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:210846400-210884600	Weak transcription	Ovary	ovary
7	chr1:210856000-210863200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:210856200-210864200	Weak transcription	Brain Substantia Nigra	brain
9	chr1:210857000-210864800	Weak transcription	Fetal Stomach	stomach
10	chr1:210857200-210882600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:210857400-210864000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:210857800-210863200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:210857800-210870800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:210858000-210864800	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:210858000-210880400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:210859800-210863800	Enhancers	HSMM	muscle
17	chr1:210859800-210865600	Weak transcription	GM12878-XiMat	blood
18	chr1:210860000-210863800	Enhancers	A549	lung
19	chr1:210860000-210863800	Enhancers	Osteobl	bone
20	chr1:210860400-210862800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:210860600-210863800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:210861000-210863200	Enhancers	HSMMtube	muscle
23	chr1:210861400-210863200	Weak transcription	NH-A	brain
24	chr1:210861600-210863200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:210861800-210862800	Enhancers	Brain Anterior Caudate	brain
26	chr1:210862000-210863200	Enhancers	Brain Hippocampus Middle	brain
27	chr1:210862000-210866000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr1:210862200-210863400	Enhancers	Brain Angular Gyrus	brain
29	chr1:210862600-210865200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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