Variant report

Variant	rs11128019
Chromosome Location	chr3:88081866-88081867
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	chr3:88073344..88075213-chr3:88081187..88083311,2	K562	blood:
4	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: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10511136	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11128018	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717413	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11915058	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714696	0.83[EUR][1000 genomes]
rs13074576	0.83[EUR][1000 genomes]
rs1431153	0.86[EUR][1000 genomes]
rs1469569	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1503433	0.83[EUR][1000 genomes]
rs1604699	0.83[EUR][1000 genomes]
rs17549213	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17549345	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1835542	0.86[EUR][1000 genomes]
rs1835543	0.83[EUR][1000 genomes]
rs2016224	0.83[EUR][1000 genomes]
rs2099229	0.83[EUR][1000 genomes]
rs2163423	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2344185	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2880801	0.83[EUR][1000 genomes]
rs2880802	0.83[EUR][1000 genomes]
rs35040143	0.86[EUR][1000 genomes]
rs4858925	0.83[EUR][1000 genomes]
rs4858969	0.83[EUR][1000 genomes]
rs4858971	0.83[EUR][1000 genomes]
rs4858972	0.83[EUR][1000 genomes]
rs4858974	0.86[EUR][1000 genomes]
rs4858975	0.86[EUR][1000 genomes]
rs55644022	0.81[ASN][1000 genomes]
rs55840331	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56006017	0.86[ASN][1000 genomes]
rs56173847	0.88[ASN][1000 genomes]
rs60099577	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551264	0.81[ASN][1000 genomes]
rs67047416	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770013	0.83[EUR][1000 genomes]
rs6778211	0.83[EUR][1000 genomes]
rs6781226	0.83[EUR][1000 genomes]
rs6781901	0.86[EUR][1000 genomes]
rs6785333	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68042814	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73144053	0.82[ASN][1000 genomes]
rs7629565	0.83[EUR][1000 genomes]
rs7630716	0.83[EUR][1000 genomes]
rs7637503	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7652406	0.83[EUR][1000 genomes]
rs9310061	0.86[EUR][1000 genomes]
rs9852704	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9855839	0.83[EUR][1000 genomes]
rs9859034	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9861809	0.83[EUR][1000 genomes]
rs9863076	0.83[EUR][1000 genomes]
rs9878862	0.83[EUR][1000 genomes]
rs9880480	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[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:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88080000-88084400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr3:88080400-88082200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:88081400-88082600	Enhancers	Fetal Thymus	thymus
4	chr3:88081600-88082200	Enhancers	Primary T cells fromperipheralblood	blood
5	chr3:88081600-88082200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:88081600-88082200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr3:88081600-88082400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:88081600-88082400	Enhancers	Primary B cells from cord blood	blood
9	chr3:88081600-88082400	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr3:88081600-88082400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr3:88081600-88082400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:88081600-88082600	Enhancers	Primary B cells from peripheral blood	blood
13	chr3:88081600-88083000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:88081600-88084000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr3:88081600-88084000	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr3:88081600-88084000	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr3:88081600-88084200	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr3:88081600-88084600	Enhancers	Primary hematopoietic stem cells	blood
19	chr3:88081600-88086800	Weak transcription	Psoas Muscle	Psoas
20	chr3:88081800-88082000	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr3:88081800-88082000	Enhancers	K562	blood
22	chr3:88081800-88082200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:88081800-88082200	Enhancers	Dnd41	blood
24	chr3:88081800-88082200	Enhancers	NHDF-Ad	bronchial
25	chr3:88081800-88082400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr3:88081800-88082400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:88081800-88082400	Enhancers	Liver	Liver
28	chr3:88081800-88082400	Active TSS	Brain Anterior Caudate	brain
29	chr3:88081800-88082600	Enhancers	Thymus	Thymus
30	chr3:88081800-88083000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:88081800-88083000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:88081800-88083000	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:88081800-88083000	Weak transcription	Brain Substantia Nigra	brain
34	chr3:88081800-88083200	Weak transcription	Primary T cells from cord blood	blood
35	chr3:88081800-88083200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:88081800-88083200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:88081800-88083200	Weak transcription	Colon Smooth Muscle	Colon
38	chr3:88081800-88083400	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr3:88081800-88083600	Weak transcription	HSMM	muscle
40	chr3:88081800-88083800	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr3:88081800-88084000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:88081800-88084000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr3:88081800-88087000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:88081800-88087000	Weak transcription	NHEK	skin
45	chr3:88081800-88091200	Weak transcription	Right Atrium	heart

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