Variant report

Variant	rs7639052
Chromosome Location	chr3:141611635-141611636
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141593025..141597254-chr3:141610097..141613194,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000069849	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1072982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13076111	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2068229	0.83[CHB][hapmap]
rs2068230	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2115937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4441632	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683645	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440043	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6440044	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6440047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440049	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6440050	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6767095	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6767302	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6773700	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790923	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7613107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7622417	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9829502	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9859932	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7639052	ATP1B3	Cis_1M	lymphoblastoid	RTeQTL
rs7639052	CLSTN2	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141596400-141626400	Weak transcription	Pancreas	Pancrea
2	chr3:141597000-141613200	Weak transcription	Placenta	Placenta
3	chr3:141597000-141615800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:141597000-141625200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr3:141597000-141646400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:141597200-141625800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr3:141597400-141618800	Weak transcription	Primary B cells from peripheral blood	blood
8	chr3:141597400-141618800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:141597800-141615800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:141597800-141617200	Weak transcription	Primary B cells from cord blood	blood
11	chr3:141597800-141617400	Weak transcription	HSMM	muscle
12	chr3:141597800-141619000	Weak transcription	Lung	lung
13	chr3:141597800-141627000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:141598000-141613800	Weak transcription	Fetal Lung	lung
15	chr3:141598000-141615800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:141598000-141618600	Weak transcription	Fetal Intestine Large	intestine
17	chr3:141598000-141618800	Weak transcription	Fetal Muscle Leg	muscle
18	chr3:141598000-141619200	Weak transcription	Psoas Muscle	Psoas
19	chr3:141598000-141625400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:141598000-141626000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:141598000-141627000	Weak transcription	Brain Hippocampus Middle	brain
22	chr3:141598000-141627200	Weak transcription	Colonic Mucosa	Colon
23	chr3:141598000-141642000	Weak transcription	Right Ventricle	heart
24	chr3:141598200-141613400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:141598200-141613400	Weak transcription	Osteobl	bone
26	chr3:141598200-141616600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:141598200-141626000	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:141598200-141627200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr3:141598200-141640200	Weak transcription	Fetal Brain Male	brain
30	chr3:141598200-141640200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr3:141598400-141613400	Weak transcription	NHLF	lung
32	chr3:141598400-141615000	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr3:141598400-141618200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:141598400-141622200	Weak transcription	Left Ventricle	heart
35	chr3:141598400-141623800	Weak transcription	NH-A	brain
36	chr3:141600400-141618800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr3:141600400-141619000	Weak transcription	Fetal Brain Female	brain
38	chr3:141600600-141613400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:141600600-141615800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr3:141600600-141619400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:141600800-141612400	Weak transcription	NHDF-Ad	bronchial
42	chr3:141600800-141614400	Weak transcription	HepG2	liver
43	chr3:141600800-141615800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:141600800-141618200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:141600800-141619000	Weak transcription	Adipose Nuclei	Adipose
46	chr3:141600800-141619000	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr3:141601200-141617200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr3:141602400-141619000	Weak transcription	Fetal Stomach	stomach
49	chr3:141604000-141617200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr3:141605200-141613400	Weak transcription	HMEC	breast

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