Variant report

Variant	rs41271539
Chromosome Location	chr1:224753353-224753354
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224701148..224701914-chr1:224753158..224753989,2	MCF-7	breast:
2	chr1:224751582..224753460-chr17:58156585..58158149,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNIH3-2	chr1:224753067-224753524	NONHSAT009815

Variant related genes	Relation type
ENSG00000267416	Chromatin interaction
ENSG00000143786	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs16849875	0.85[EUR][1000 genomes]
rs16850015	0.82[EUR][1000 genomes]
rs16850250	0.80[AMR][1000 genomes];0.82[EUR][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	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv873224	chr1:224746577-224794913	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224740000-224762200	Weak transcription	Ovary	ovary
2	chr1:224750000-224754000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:224750000-224754000	Enhancers	HMEC	breast
4	chr1:224750400-224754000	Enhancers	NHEK	skin
5	chr1:224750800-224753600	Enhancers	HSMMtube	muscle
6	chr1:224751200-224753400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:224751400-224754200	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr1:224751600-224753600	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr1:224751800-224753800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:224752000-224753600	Enhancers	Psoas Muscle	Psoas
11	chr1:224752000-224753800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:224752200-224753600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:224752200-224753600	Enhancers	Esophagus	oesophagus
14	chr1:224752200-224753600	Enhancers	NHLF	lung
15	chr1:224752200-224753800	Enhancers	HSMM	muscle
16	chr1:224752200-224753800	Enhancers	HUVEC	blood vessel
17	chr1:224752200-224753800	Enhancers	NH-A	brain
18	chr1:224752200-224753800	Enhancers	Osteobl	bone
19	chr1:224752400-224753400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:224752400-224753600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:224752400-224753800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:224752400-224754000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:224752600-224753400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr1:224752600-224753600	Enhancers	A549	lung
25	chr1:224752600-224753800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:224752800-224753400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:224753000-224753600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:224753000-224753600	Enhancers	Pancreas	Pancrea
29	chr1:224753200-224753600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:224753200-224753600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:224753200-224753600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:224753200-224753600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:224753200-224753600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr1:224753200-224753600	Flanking Active TSS	Hela-S3	cervix
35	chr1:224753200-224753600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr1:224753200-224753600	Flanking Active TSS	NHDF-Ad	bronchial
37	chr1:224753200-224753800	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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