Variant report

Variant	rs6772987
Chromosome Location	chr3:160105758-160105759
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160102108..160105974-chr3:160114282..160119740,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113810	Chromatin interaction
ENSG00000068885	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs2015054	1.00[AMR][1000 genomes]
rs2015065	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3773371	0.81[YRI][hapmap]
rs55815116	0.83[AFR][1000 genomes]
rs56150006	0.88[AFR][1000 genomes]
rs59700052	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60304551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60703878	1.00[AFR][1000 genomes]
rs60824140	1.00[AMR][1000 genomes]
rs62272181	0.88[AFR][1000 genomes]
rs62272185	0.88[AFR][1000 genomes]
rs62272197	0.88[AFR][1000 genomes]
rs6441307	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs66769612	0.88[AFR][1000 genomes]
rs6764107	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7611148	0.94[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7611573	0.87[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7618017	0.88[AFR][1000 genomes]
rs7631284	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	esv1801474	chr3:160012843-160153305	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	206 gene(s)	inside rSNPs	diseases
7	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
8	esv1795255	chr3:160089896-160153305	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	205 gene(s)	inside rSNPs	diseases
9	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160061400-160109600	Weak transcription	Fetal Heart	heart
2	chr3:160069000-160115200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:160073800-160108400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:160076200-160116200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:160083400-160113000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:160083800-160108200	Weak transcription	GM12878-XiMat	blood
7	chr3:160083800-160116000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:160088800-160108600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:160088800-160108600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:160088800-160116200	Weak transcription	Primary B cells from cord blood	blood
11	chr3:160088800-160116200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:160091600-160105800	Weak transcription	Ovary	ovary
13	chr3:160092000-160113200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:160092200-160116000	Weak transcription	Fetal Stomach	stomach
15	chr3:160092200-160116200	Weak transcription	Fetal Intestine Small	intestine
16	chr3:160092200-160116600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:160093000-160113000	Weak transcription	NHLF	lung
18	chr3:160093200-160113200	Weak transcription	Brain Germinal Matrix	brain
19	chr3:160093600-160116000	Weak transcription	Fetal Kidney	kidney
20	chr3:160094600-160116000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:160094800-160113000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:160094800-160113200	Weak transcription	HSMM	muscle
23	chr3:160094800-160115800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr3:160094800-160116000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:160094800-160116000	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:160094800-160116600	Weak transcription	Left Ventricle	heart
27	chr3:160095000-160115800	Weak transcription	Fetal Intestine Large	intestine
28	chr3:160095000-160116000	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:160095200-160108400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr3:160095200-160115000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr3:160095400-160108600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr3:160095400-160113200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:160095400-160116000	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr3:160097000-160113200	Weak transcription	A549	lung
35	chr3:160098200-160113400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:160098400-160107200	Weak transcription	HMEC	breast
37	chr3:160098400-160113400	Weak transcription	Dnd41	blood
38	chr3:160098400-160115200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:160098400-160116200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr3:160098400-160116400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr3:160098800-160115600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr3:160098800-160115800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:160098800-160116200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:160099000-160108600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:160099000-160113200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr3:160099400-160113200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:160099400-160116000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:160100000-160113000	Weak transcription	Osteobl	bone
49	chr3:160100200-160113000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:160102400-160108200	Weak transcription	Stomach Mucosa	stomach

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