Variant report

Variant	rs7699718
Chromosome Location	chr4:78879461-78879462
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	chr4:78739575..78741919-chr4:78878334..78880056,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138767	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11932644	0.84[EUR][1000 genomes]
rs11935318	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11941918	0.90[EUR][1000 genomes]
rs17002830	0.90[EUR][1000 genomes]
rs17409255	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs17409708	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs17409820	0.90[EUR][1000 genomes]
rs17410182	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17416711	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17416836	1.00[CEU][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17449827	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs17450307	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs17450474	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17450655	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1801350	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1801521	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1915587	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs1915588	1.00[CEU][hapmap];0.88[YRI][hapmap];0.90[EUR][1000 genomes]
rs41437548	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs57408981	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58449376	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6810599	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6812768	0.94[EUR][1000 genomes]
rs6815466	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6816113	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs6825764	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6850795	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6853446	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7656101	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7657481	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs7657902	0.94[EUR][1000 genomes]
rs7673193	1.00[CEU][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7674271	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs7678283	1.00[CEU][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7687500	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752050	chr4:78693311-78975321	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1010714	chr4:78742505-78991030	Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv516836	chr4:78748977-78981919	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv594704	chr4:78748977-78981919	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv461562	chr4:78757015-78981919	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv461563	chr4:78757015-78981919	Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv594705	chr4:78757015-78981919	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1008217	chr4:78777531-78957311	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv537145	chr4:78777531-78957311	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78806000-78881000	Weak transcription	Brain Hippocampus Middle	brain
2	chr4:78809600-78881200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:78849600-78881000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr4:78850200-78881000	Weak transcription	A549	lung
5	chr4:78852000-78881200	Weak transcription	Lung	lung
6	chr4:78853200-78880800	Weak transcription	Osteobl	bone
7	chr4:78853200-78881000	Weak transcription	Brain Anterior Caudate	brain
8	chr4:78863400-78880800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:78865800-78881000	Weak transcription	Psoas Muscle	Psoas
10	chr4:78866800-78881000	Weak transcription	Fetal Kidney	kidney
11	chr4:78868600-78881000	Weak transcription	Brain Angular Gyrus	brain
12	chr4:78869000-78879600	Weak transcription	Spleen	Spleen
13	chr4:78870400-78881000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr4:78872400-78880800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr4:78872600-78880800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr4:78873400-78881200	Weak transcription	Left Ventricle	heart
17	chr4:78874200-78881000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr4:78874200-78884400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr4:78874800-78881200	Weak transcription	Brain Substantia Nigra	brain
20	chr4:78875200-78881200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr4:78875200-78883800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr4:78875400-78881000	Weak transcription	HSMM	muscle
23	chr4:78875400-78884000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr4:78876000-78881000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:78876000-78881000	Weak transcription	Fetal Lung	lung
26	chr4:78876000-78883400	Weak transcription	Thymus	Thymus
27	chr4:78876000-78884000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:78876200-78880800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:78876200-78880800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:78876200-78880800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr4:78876200-78881000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr4:78876200-78881000	Weak transcription	Aorta	Aorta
33	chr4:78876200-78881000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr4:78876200-78881000	Weak transcription	Ovary	ovary
35	chr4:78876200-78881200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr4:78876200-78881200	Weak transcription	NH-A	brain
37	chr4:78876200-78884000	Weak transcription	Primary T cells from cord blood	blood
38	chr4:78876200-78884000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr4:78876200-78884200	Weak transcription	Fetal Thymus	thymus
40	chr4:78876400-78880800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr4:78876400-78881200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr4:78876600-78881200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr4:78877000-78880200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr4:78878000-78881000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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