Variant report

Variant	rs6540840
Chromosome Location	chr1:214657331-214657332
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:214656600..214658506-chr1:214723643..214725822,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152104	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10746445	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10746446	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11120334	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4130486	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4233305	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4233307	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4253891	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4301608	0.83[EUR][1000 genomes]
rs4421564	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4451529	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4465172	0.83[EUR][1000 genomes]
rs4539105	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6540831	0.83[EUR][1000 genomes]
rs6540836	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6540839	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665797	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6682987	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7528679	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7528775	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7528800	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7535598	0.83[EUR][1000 genomes]
rs7537159	0.82[ASN][1000 genomes]
rs7537274	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555415	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[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	nsv468094	chr1:214654965-214687725	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv549180	chr1:214654965-214687725	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214641400-214667800	Weak transcription	Hela-S3	cervix
2	chr1:214645800-214666000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr1:214646000-214672200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:214647200-214661600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:214648000-214669400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:214649200-214660800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:214650200-214657400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:214650200-214658000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:214650200-214666000	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:214650600-214657400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:214650800-214657400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:214650800-214660000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:214650800-214662600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:214651000-214666400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:214651200-214657400	Weak transcription	Psoas Muscle	Psoas
16	chr1:214651200-214659400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:214651200-214664600	Weak transcription	Left Ventricle	heart
18	chr1:214651200-214665600	Weak transcription	NHLF	lung
19	chr1:214651200-214666000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:214651200-214666400	Weak transcription	Adipose Nuclei	Adipose
21	chr1:214651600-214661400	Weak transcription	Fetal Heart	heart
22	chr1:214651800-214658000	Weak transcription	NH-A	brain
23	chr1:214651800-214663000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr1:214651800-214665400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:214651800-214668000	Weak transcription	HSMMtube	muscle
26	chr1:214652000-214665800	Weak transcription	NHDF-Ad	bronchial
27	chr1:214652000-214666000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:214652200-214658000	Weak transcription	HSMM	muscle
29	chr1:214652200-214664800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:214652600-214657400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:214652600-214662000	Weak transcription	HUVEC	blood vessel
32	chr1:214654400-214677400	Weak transcription	Gastric	stomach
33	chr1:214654600-214658400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:214655600-214657400	Enhancers	Osteobl	bone
35	chr1:214655600-214659000	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr1:214655800-214658400	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr1:214656000-214658200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr1:214656200-214657400	Enhancers	Colon Smooth Muscle	Colon
39	chr1:214656200-214657600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:214656200-214658000	Enhancers	NHEK	skin
41	chr1:214656200-214658200	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr1:214656200-214658600	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr1:214656400-214658400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:214656400-214658800	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr1:214656400-214660200	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr1:214656600-214658000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr1:214656600-214660200	Enhancers	H1 Cell Line	embryonic stem cell
48	chr1:214656800-214664600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:214656800-214665800	Weak transcription	HMEC	breast
50	chr1:214656800-214667800	Weak transcription	A549	lung

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