Variant report

Variant	rs3772980
Chromosome Location	chr3:69153481-69153482
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:69133410..69135545-chr3:69153469..69155748,2	MCF-7	breast:
2	chr3:69153444..69155316-chr3:69160247..69161792,2	MCF-7	breast:
3	chr3:69151962..69153673-chr3:69157570..69159178,2	K562	blood:
4	chr3:69134734..69136493-chr3:69152405..69154710,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144746	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10489	0.82[ASW][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.94[MKK][hapmap];0.95[YRI][hapmap];0.80[ASN][1000 genomes]
rs1051901	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1131960	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12054346	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13090606	0.86[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.83[MKK][hapmap]
rs17005366	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2009602	0.81[CHB][hapmap]
rs2271118	0.80[JPT][hapmap]
rs2271122	0.81[CHB][hapmap]
rs2292199	0.86[CHB][hapmap];0.81[CHD][hapmap];0.83[MKK][hapmap]
rs3772979	0.81[CHB][hapmap]
rs3772983	1.00[EUR][1000 genomes]
rs3796213	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs3796214	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs3821562	0.81[CHB][hapmap]
rs3821564	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3853157	0.81[CHB][hapmap]
rs4525874	0.81[GIH][hapmap];1.00[MEX][hapmap]
rs56152276	1.00[EUR][1000 genomes]
rs56194306	1.00[EUR][1000 genomes]
rs56280964	1.00[EUR][1000 genomes]
rs57159802	1.00[EUR][1000 genomes]
rs58277851	1.00[EUR][1000 genomes]
rs59090383	1.00[EUR][1000 genomes]
rs60230066	0.97[ASN][1000 genomes]
rs60474520	1.00[EUR][1000 genomes]
rs6549181	0.81[CHB][hapmap]
rs6549184	0.93[CHB][hapmap];0.89[GIH][hapmap]
rs6777032	0.81[CHB][hapmap]
rs72924853	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72924854	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73835722	1.00[EUR][1000 genomes]
rs73835726	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73835727	1.00[EUR][1000 genomes]
rs73835728	1.00[EUR][1000 genomes]
rs73835729	1.00[EUR][1000 genomes]
rs7617775	0.86[EUR][1000 genomes]
rs7621394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621929	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625579	0.93[CHB][hapmap];0.80[ASN][1000 genomes]
rs7627893	0.80[ASN][1000 genomes]
rs7629932	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs937863	0.85[GIH][hapmap]

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	nsv876933	chr3:69059023-69227379	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv876934	chr3:69111512-69166895	Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 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	chr3:69135200-69155200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:69135800-69155800	Weak transcription	Fetal Kidney	kidney
3	chr3:69136800-69156400	Weak transcription	Fetal Brain Male	brain
4	chr3:69139800-69154600	Weak transcription	A549	lung
5	chr3:69142000-69160400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:69143600-69160200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:69145600-69153600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:69145600-69160200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:69145800-69160200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:69146200-69160200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:69147400-69160200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:69147800-69153600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:69148000-69153800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
14	chr3:69148600-69153800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:69148600-69155200	Strong transcription	Primary B cells from cord blood	blood
16	chr3:69148600-69155800	Strong transcription	Primary B cells from peripheral blood	blood
17	chr3:69148800-69153800	Strong transcription	Fetal Muscle Trunk	muscle
18	chr3:69148800-69154000	Strong transcription	Fetal Muscle Leg	muscle
19	chr3:69148800-69155600	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr3:69148800-69155600	Strong transcription	GM12878-XiMat	blood
21	chr3:69148800-69155800	Strong transcription	Duodenum Mucosa	Duodenum
22	chr3:69148800-69155800	Strong transcription	Dnd41	blood
23	chr3:69149000-69154800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:69149200-69154200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:69149200-69155400	Strong transcription	Fetal Thymus	thymus
26	chr3:69149600-69154000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:69150000-69155400	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr3:69150200-69154800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:69150200-69155400	Strong transcription	NH-A	brain
30	chr3:69150400-69154000	Strong transcription	HSMMtube	muscle
31	chr3:69150400-69155800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:69150600-69154000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:69150600-69154000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:69150600-69154000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:69150600-69154000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
36	chr3:69150600-69154000	Strong transcription	Thymus	Thymus
37	chr3:69150600-69154200	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:69150600-69154200	Strong transcription	NHLF	lung
39	chr3:69150600-69154400	Strong transcription	Adipose Nuclei	Adipose
40	chr3:69150600-69155600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:69150600-69155800	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr3:69150800-69153600	Strong transcription	NHDF-Ad	bronchial
43	chr3:69150800-69153600	Strong transcription	Osteobl	bone
44	chr3:69150800-69154200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:69150800-69154200	Strong transcription	Fetal Intestine Large	intestine
46	chr3:69150800-69154400	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:69150800-69154400	Strong transcription	Fetal Lung	lung
48	chr3:69150800-69155600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:69150800-69155800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:69150800-69155800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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