Variant report

Variant	rs55883959
Chromosome Location	chr3:88116071-88116072
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:88104108..88106315-chr3:88113746..88116261,2	MCF-7	breast:
2	chr3:88105473..88111150-chr3:88112060..88119652,14	K562	blood:
3	chr3:88114310..88116574-chr3:88119594..88122386,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163320	Chromatin interaction
ENSG00000229729	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1006896	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10858	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11925988	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13317202	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2735556	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2735559	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4858934	0.81[ASN][1000 genomes]
rs4858939	0.86[AFR][1000 genomes]
rs4859003	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs55928667	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs55932154	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs56185750	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs56211058	0.81[ASN][1000 genomes]
rs56246133	0.81[ASN][1000 genomes]
rs6419868	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6551276	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6551281	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6551287	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs73132512	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs73132546	0.81[ASN][1000 genomes]
rs73146085	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73146095	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73146099	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73148006	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7430022	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7432826	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7650068	0.81[ASN][1000 genomes]
rs9826925	0.86[AFR][1000 genomes];0.81[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	nsv916330	chr3:88083580-88884125	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55883959	CGGBP1///LOC728397	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88109400-88124400	Weak transcription	Pancreas	Pancrea
2	chr3:88110000-88116600	Weak transcription	Thymus	Thymus
3	chr3:88110000-88118600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:88110000-88120400	Weak transcription	Fetal Stomach	stomach
5	chr3:88110000-88120400	Weak transcription	Fetal Thymus	thymus
6	chr3:88110000-88121000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr3:88110200-88117200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:88110200-88124200	Weak transcription	Fetal Kidney	kidney
9	chr3:88110400-88120200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:88111200-88117800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:88111400-88116400	Weak transcription	Right Ventricle	heart
12	chr3:88111400-88117200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:88111400-88121600	Weak transcription	Fetal Brain Male	brain
14	chr3:88111400-88124200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr3:88111400-88133600	Weak transcription	Brain Angular Gyrus	brain
16	chr3:88111400-88136200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:88111400-88136200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:88111600-88116400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:88111600-88116800	Weak transcription	Primary B cells from cord blood	blood
20	chr3:88111600-88116800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:88111600-88118000	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr3:88111600-88119800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:88111600-88121200	Weak transcription	NHLF	lung
24	chr3:88111600-88123200	Weak transcription	Liver	Liver
25	chr3:88111600-88124000	Weak transcription	Right Atrium	heart
26	chr3:88111600-88124000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:88111600-88124000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr3:88111600-88124200	Weak transcription	Fetal Lung	lung
29	chr3:88111600-88135200	Weak transcription	HSMM	muscle
30	chr3:88111600-88135400	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr3:88111600-88135600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:88111800-88123600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr3:88111800-88135400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:88112200-88136600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:88112200-88154200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr3:88112400-88116400	Weak transcription	Aorta	Aorta
37	chr3:88112400-88117200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:88112400-88117200	Weak transcription	Fetal Heart	heart
39	chr3:88112400-88121200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:88112400-88124400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr3:88112400-88143600	Weak transcription	HUVEC	blood vessel
42	chr3:88112600-88116400	Weak transcription	Psoas Muscle	Psoas
43	chr3:88113000-88117200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:88113200-88116200	Weak transcription	K562	blood
45	chr3:88113200-88146200	Weak transcription	HMEC	breast
46	chr3:88113600-88117400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr3:88113600-88121400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:88113800-88116200	Weak transcription	Colon Smooth Muscle	Colon
49	chr3:88113800-88116400	Weak transcription	Brain Hippocampus Middle	brain
50	chr3:88113800-88116400	Weak transcription	Ovary	ovary

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