Variant report

Variant	rs13066048
Chromosome Location	chr3:45982414-45982415
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr3:45982373-45982445	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr3:45982382-45982432	MCF10A-Er-Src	breast:	n/a	n/a
3	USF1	chr3:45982272-45982461	H1-hESC	embryonic stem cell:	n/a	n/a
4	FOS	chr3:45982274-45982526	MCF10A-Er-Src	breast:	n/a	n/a
5	CBX3	chr3:45982132-45982536	K562	blood:	n/a	n/a
6	SETDB1	chr3:45982089-45982554	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:45979978..45982491-chr3:46035904..46038054,2	MCF-7	breast:

Variant related genes	Relation type
CXCR6	TF binding region
ENSG00000163820	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1072755	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130080	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs12495073	0.92[CEU][hapmap]
rs12630101	1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12635494	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12635657	1.00[CEU][hapmap]
rs12639598	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13073861	0.84[CEU][hapmap]
rs13091821	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13091979	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1532071	0.93[ASN][1000 genomes]
rs1552489	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1552490	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1601867	0.95[ASN][1000 genomes]
rs17078449	0.85[CHB][hapmap]
rs17078454	0.81[ASN][1000 genomes]
rs1994488	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1994489	0.93[ASN][1000 genomes]
rs1994490	0.80[CHB][hapmap];0.83[ASN][1000 genomes]
rs2054866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2131091	0.84[CEU][hapmap]
rs2171530	0.84[ASN][1000 genomes]
rs2234351	0.81[ASN][1000 genomes]
rs2234358	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2248228	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2291470	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2373154	0.92[CEU][hapmap]
rs35465473	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3733100	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs3733103	0.92[CEU][hapmap];0.82[CHB][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3774634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3774635	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3774638	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs3774639	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774640	0.81[ASN][1000 genomes]
rs3796373	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs3796375	0.96[CEU][hapmap];0.80[CHB][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3821884	0.80[CHB][hapmap]
rs4535265	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682799	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4682800	0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs4683147	0.83[CEU][hapmap]
rs4683148	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4683149	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683152	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683154	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683156	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4683157	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57204020	0.81[ASN][1000 genomes]
rs6778896	0.82[EUR][1000 genomes]
rs6800954	0.80[CHB][hapmap]
rs7129	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs730983	0.96[CEU][hapmap]
rs737452	0.96[CEU][hapmap]
rs751552	0.96[CEU][hapmap];0.80[CHB][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs751553	0.96[CEU][hapmap];0.80[CHB][hapmap];0.82[EUR][1000 genomes]
rs9311380	0.93[ASN][1000 genomes]
rs936938	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs936939	0.90[CHB][hapmap]
rs9824253	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9831315	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45958800-45988000	Weak transcription	HUVEC	blood vessel
2	chr3:45959400-46009800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:45963200-45985200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:45970200-45988200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:45972800-45988600	Weak transcription	Small Intestine	intestine
6	chr3:45973400-45986400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:45973800-45988000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:45973800-45991400	Weak transcription	Brain Germinal Matrix	brain
9	chr3:45974400-45988000	Weak transcription	Fetal Kidney	kidney
10	chr3:45977400-45987000	Weak transcription	Fetal Lung	lung
11	chr3:45977400-45988000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:45977600-45983400	Weak transcription	Primary B cells from cord blood	blood
13	chr3:45977600-45987600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:45978000-45988000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:45978200-45988200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:45978400-45983800	Weak transcription	Spleen	Spleen
17	chr3:45978400-45986600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:45978800-45982800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:45978800-45994400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:45979000-45987200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:45979000-45988200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:45979000-45993000	Weak transcription	Stomach Mucosa	stomach
23	chr3:45979200-45987200	Weak transcription	Colonic Mucosa	Colon
24	chr3:45979200-45987800	Weak transcription	Brain Anterior Caudate	brain
25	chr3:45979200-45987800	Weak transcription	HepG2	liver
26	chr3:45979200-45988200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:45979400-45983200	Weak transcription	Pancreas	Pancrea
28	chr3:45979600-45983200	Weak transcription	Esophagus	oesophagus
29	chr3:45979600-45984200	Weak transcription	Liver	Liver
30	chr3:45979800-45983200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:45979800-45983600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr3:45979800-45983600	Weak transcription	Gastric	stomach
33	chr3:45980200-45982600	Genic enhancers	Dnd41	blood
34	chr3:45980200-45984800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
35	chr3:45980400-45984800	Enhancers	Placenta	Placenta
36	chr3:45980600-45984000	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr3:45980800-45983600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr3:45980800-45983600	Weak transcription	Adipose Nuclei	Adipose
39	chr3:45980800-45983800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr3:45980800-45984400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr3:45980800-45986800	Weak transcription	Primary B cells from peripheral blood	blood
42	chr3:45980800-45988000	Weak transcription	NH-A	brain
43	chr3:45980800-45989200	Weak transcription	Fetal Brain Male	brain
44	chr3:45980800-46013400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:45981000-45983200	Weak transcription	Fetal Muscle Leg	muscle
46	chr3:45981000-45983200	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr3:45981000-45983400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr3:45981000-45983600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr3:45981000-45983800	Weak transcription	Right Atrium	heart
50	chr3:45981000-45986400	Weak transcription	Rectal Smooth Muscle	rectum

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