Variant report

Variant	rs7624456
Chromosome Location	chr3:141601718-141601719
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141456610..141459064-chr3:141599182..141601879,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114125	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11915071	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11926859	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2068231	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2115938	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28454329	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28463227	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4511872	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58370035	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6440048	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6767100	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6773662	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6782993	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6801868	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804938	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805115	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806440	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73230628	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7616510	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7642890	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648330	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849347	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853609	0.87[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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3333253	chr3:141585303-141602936	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7624456	ATP1B3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141596400-141609400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:141596400-141626400	Weak transcription	Pancreas	Pancrea
3	chr3:141597000-141604600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:141597000-141613200	Weak transcription	Placenta	Placenta
5	chr3:141597000-141615800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:141597000-141625200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:141597000-141646400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:141597200-141625800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:141597400-141618800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr3:141597400-141618800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:141597800-141604200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:141597800-141606000	Weak transcription	Aorta	Aorta
13	chr3:141597800-141615800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:141597800-141617200	Weak transcription	Primary B cells from cord blood	blood
15	chr3:141597800-141617400	Weak transcription	HSMM	muscle
16	chr3:141597800-141619000	Weak transcription	Lung	lung
17	chr3:141597800-141627000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:141598000-141605600	Weak transcription	HSMMtube	muscle
19	chr3:141598000-141613800	Weak transcription	Fetal Lung	lung
20	chr3:141598000-141615800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:141598000-141618600	Weak transcription	Fetal Intestine Large	intestine
22	chr3:141598000-141618800	Weak transcription	Fetal Muscle Leg	muscle
23	chr3:141598000-141619200	Weak transcription	Psoas Muscle	Psoas
24	chr3:141598000-141625400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:141598000-141626000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:141598000-141627000	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:141598000-141627200	Weak transcription	Colonic Mucosa	Colon
28	chr3:141598000-141642000	Weak transcription	Right Ventricle	heart
29	chr3:141598200-141603000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr3:141598200-141613400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:141598200-141613400	Weak transcription	Osteobl	bone
32	chr3:141598200-141616600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:141598200-141626000	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:141598200-141627200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr3:141598200-141640200	Weak transcription	Fetal Brain Male	brain
36	chr3:141598200-141640200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr3:141598400-141604400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:141598400-141607000	Weak transcription	Small Intestine	intestine
39	chr3:141598400-141613400	Weak transcription	NHLF	lung
40	chr3:141598400-141615000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr3:141598400-141618200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:141598400-141622200	Weak transcription	Left Ventricle	heart
43	chr3:141598400-141623800	Weak transcription	NH-A	brain
44	chr3:141598600-141606400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:141599200-141601800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:141599200-141604600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:141599200-141609600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:141599400-141604400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr3:141599400-141604600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr3:141599400-141604800	Weak transcription	HMEC	breast

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