Variant report

Variant	rs1469570
Chromosome Location	chr3:88080655-88080656
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:88079170..88082380-chr3:88083202..88085793,3	MCF-7	breast:
2	chr3:88080562..88082885-chr3:88098755..88100923,2	MCF-7	breast:
3	chr3:88079258..88082127-chr3:88106343..88109218,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229729	Chromatin interaction
ENSG00000163320	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12632860	1.00[ASN][1000 genomes]
rs1431154	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1431155	1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1431156	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1594453	1.00[ASN][1000 genomes]
rs1594455	1.00[ASN][1000 genomes]
rs1604700	1.00[ASN][1000 genomes]
rs1835544	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1897238	1.00[ASN][1000 genomes]
rs2033390	1.00[ASN][1000 genomes]
rs2344183	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2344184	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2880793	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915287	1.00[CHB][hapmap]
rs4431134	1.00[CHB][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4515075	1.00[ASN][1000 genomes]
rs4616669	1.00[ASN][1000 genomes]
rs4858927	1.00[ASN][1000 genomes]
rs4858970	1.00[ASN][1000 genomes]
rs6301	0.83[EUR][1000 genomes]
rs6767497	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650749	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs891597	1.00[CHB][hapmap]
rs919582	0.86[AFR][1000 genomes]
rs930154	1.00[ASN][1000 genomes]
rs930155	0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310062	1.00[ASN][1000 genomes]
rs9310063	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9310064	1.00[ASN][1000 genomes]
rs9812903	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9833231	1.00[ASN][1000 genomes]
rs9850550	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9854250	1.00[CHB][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867614	1.00[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	nsv877146	chr3:87983962-88159835	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	nsv536635	chr3:88049304-88088520	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88078200-88080800	Weak transcription	Left Ventricle	heart
2	chr3:88079200-88081400	Active TSS	GM12878-XiMat	blood
3	chr3:88079400-88081800	Active TSS	NHDF-Ad	bronchial
4	chr3:88079600-88080800	Enhancers	HepG2	liver
5	chr3:88079800-88080800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr3:88079800-88080800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:88079800-88080800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr3:88079800-88080800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:88080000-88081200	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr3:88080000-88084400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:88080400-88080800	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr3:88080400-88080800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr3:88080400-88080800	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr3:88080400-88080800	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr3:88080400-88080800	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr3:88080400-88080800	Enhancers	Hela-S3	cervix
17	chr3:88080400-88081000	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr3:88080400-88081000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:88080400-88081000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr3:88080400-88081000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr3:88080400-88081200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:88080400-88081600	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr3:88080400-88081600	Active TSS	Brain Angular Gyrus	brain
24	chr3:88080400-88081600	Active TSS	Brain Anterior Caudate	brain
25	chr3:88080400-88081600	Active TSS	K562	blood
26	chr3:88080400-88081800	Active TSS	Brain Hippocampus Middle	brain
27	chr3:88080400-88081800	Flanking Active TSS	Dnd41	blood
28	chr3:88080400-88081800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr3:88080400-88082200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:88080600-88080800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:88080600-88080800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr3:88080600-88080800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr3:88080600-88080800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:88080600-88080800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:88080600-88080800	Enhancers	Brain Germinal Matrix	brain
36	chr3:88080600-88080800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
37	chr3:88080600-88080800	Enhancers	Colonic Mucosa	Colon
38	chr3:88080600-88080800	Flanking Active TSS	Colon Smooth Muscle	Colon
39	chr3:88080600-88080800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr3:88080600-88080800	Enhancers	Fetal Kidney	kidney
41	chr3:88080600-88080800	Flanking Active TSS	Stomach Mucosa	stomach
42	chr3:88080600-88080800	Flanking Active TSS	A549	lung
43	chr3:88080600-88080800	Enhancers	HMEC	breast
44	chr3:88080600-88080800	Flanking Active TSS	NHLF	lung
45	chr3:88080600-88081000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:88080600-88081000	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr3:88080600-88081000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr3:88080600-88081000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:88080600-88081000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:88080600-88081000	Flanking Active TSS	Adipose Nuclei	Adipose

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