Variant report

Variant	rs4652540
Chromosome Location	chr1:180922008-180922009
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:180921716..180926405-chr1:180990463..180993659,6	MCF-7	breast:
2	chr1:180920141..180924832-chr1:180927695..180934337,6	MCF-7	breast:
3	chr1:180921700..180925041-chr1:180990802..180993603,10	MCF-7	breast:
4	chr1:180913861..180917662-chr1:180919365..180922791,5	K562	blood:
5	chr1:180918890..180922237-chr1:180924310..180927954,4	K562	blood:
6	chr1:180894020..180896970-chr1:180921543..180923993,2	MCF-7	breast:
7	chr1:180921489..180923428-chr1:180979617..180981443,2	MCF-7	breast:
8	chr1:180914551..180916249-chr1:180920507..180922791,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000135823	Chromatin interaction
ENSG00000251520	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	0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2297184	0.96[ASN][1000 genomes]
rs3820313	0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4652542	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];0.93[ASN][1000 genomes]
rs870046	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	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:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180899000-180922600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr1:180900000-180922800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:180904800-180922400	Weak transcription	Colonic Mucosa	Colon
4	chr1:180905400-180922400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:180905400-180940600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:180907800-180922400	Weak transcription	NHDF-Ad	bronchial
7	chr1:180911600-180928400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:180911800-180927600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:180912400-180922400	Weak transcription	Stomach Mucosa	stomach
10	chr1:180914800-180922600	Weak transcription	Ovary	ovary
11	chr1:180915400-180922800	Enhancers	Placenta Amnion	Placenta Amnion
12	chr1:180915600-180922400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:180916200-180922600	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:180916400-180922400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:180916400-180922600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr1:180916400-180922600	Weak transcription	HSMM	muscle
17	chr1:180916800-180922200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:180916800-180922600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr1:180916800-180922600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:180917000-180922400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:180917200-180922800	Enhancers	Placenta	Placenta
22	chr1:180917400-180922800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr1:180917600-180922600	Weak transcription	Brain Germinal Matrix	brain
24	chr1:180917800-180922400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr1:180917800-180922400	Weak transcription	NHEK	skin
26	chr1:180918000-180930000	Weak transcription	HSMMtube	muscle
27	chr1:180918200-180922600	Weak transcription	Primary B cells from cord blood	blood
28	chr1:180918200-180922800	Weak transcription	Psoas Muscle	Psoas
29	chr1:180918400-180922400	Weak transcription	HMEC	breast
30	chr1:180918400-180929000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr1:180918400-180929800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:180918400-180930000	Weak transcription	Hela-S3	cervix
33	chr1:180918600-180939800	Weak transcription	K562	blood
34	chr1:180918600-180944800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:180919000-180925000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:180919400-180922400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:180919600-180922400	Weak transcription	A549	lung
38	chr1:180919600-180923600	Weak transcription	Fetal Kidney	kidney
39	chr1:180919800-180922400	Weak transcription	Brain Substantia Nigra	brain
40	chr1:180919800-180922400	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr1:180919800-180922600	Enhancers	Adipose Nuclei	Adipose
42	chr1:180919800-180922600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:180919800-180928800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr1:180919800-180935800	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr1:180920000-180922400	Weak transcription	Fetal Brain Male	brain
46	chr1:180920000-180922400	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr1:180920000-180922600	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr1:180920000-180922600	Enhancers	Brain Angular Gyrus	brain
49	chr1:180920000-180922600	Weak transcription	Left Ventricle	heart
50	chr1:180920000-180922800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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