Variant report

Variant	rs4652542
Chromosome Location	chr1:180929200-180929201
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180924451..180927761-chr1:180928276..180933255,6	MCF-7	breast:
2	chr1:180927440..180930124-chr1:180947176..180950127,2	MCF-7	breast:
3	chr1:180920141..180924832-chr1:180927695..180934337,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232586	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11799738	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2297184	0.95[ASN][1000 genomes]
rs3820313	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4652540	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71630288	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs870046	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv872579	chr1:180881148-180931508	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2754938	chr1:180919343-180934343	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180905400-180940600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:180918000-180930000	Weak transcription	HSMMtube	muscle
3	chr1:180918400-180929800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:180918400-180930000	Weak transcription	Hela-S3	cervix
5	chr1:180918600-180939800	Weak transcription	K562	blood
6	chr1:180918600-180944800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:180919800-180935800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:180922200-180929200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:180922600-180949400	Strong transcription	Dnd41	blood
10	chr1:180923000-180935800	Weak transcription	Fetal Heart	heart
11	chr1:180923600-180944800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:180923600-180958800	Weak transcription	Small Intestine	intestine
13	chr1:180923800-180930000	Weak transcription	HSMM	muscle
14	chr1:180923800-180933400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr1:180923800-180938600	Weak transcription	Aorta	Aorta
16	chr1:180923800-180942800	Weak transcription	Fetal Lung	lung
17	chr1:180923800-180944800	Weak transcription	HUVEC	blood vessel
18	chr1:180923800-180944800	Weak transcription	NH-A	brain
19	chr1:180924000-180930400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:180924000-180930800	Weak transcription	Fetal Kidney	kidney
21	chr1:180924000-180932800	Weak transcription	Lung	lung
22	chr1:180924000-180933800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:180924000-180934000	Weak transcription	Spleen	Spleen
24	chr1:180924000-180934400	Weak transcription	Left Ventricle	heart
25	chr1:180924000-180935000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:180924000-180935600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr1:180924000-180937800	Weak transcription	Right Ventricle	heart
28	chr1:180924000-180938400	Weak transcription	NHLF	lung
29	chr1:180924000-180938800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:180924000-180939000	Weak transcription	Colonic Mucosa	Colon
31	chr1:180924000-180939200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr1:180924000-180939400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:180924000-180940000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:180924000-180940200	Weak transcription	Gastric	stomach
35	chr1:180924000-180941600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:180924200-180929200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:180924200-180929400	Weak transcription	A549	lung
38	chr1:180924200-180930000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr1:180924200-180930800	Weak transcription	Ovary	ovary
40	chr1:180924200-180931200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:180924200-180931200	Weak transcription	Placenta	Placenta
42	chr1:180924200-180931400	Weak transcription	Osteobl	bone
43	chr1:180924200-180933400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:180924200-180934400	Weak transcription	GM12878-XiMat	blood
45	chr1:180924200-180935000	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:180924200-180936200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr1:180924200-180939000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr1:180924200-180940000	Weak transcription	NHDF-Ad	bronchial
49	chr1:180924200-180941600	Weak transcription	Pancreas	Pancrea
50	chr1:180924200-180942000	Weak transcription	Liver	Liver

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