Variant report

Variant	rs4425287
Chromosome Location	chr3:88114399-88114400
allele	C/T
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:
4	chr3:88106854..88110640-chr3:88110801..88115329,7	K562	blood:

Variant related genes	Relation type
ENSG00000163320	Chromatin interaction
ENSG00000229729	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11128023	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1367615	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1431154	1.00[EUR][1000 genomes]
rs1594453	1.00[EUR][1000 genomes]
rs1594455	1.00[EUR][1000 genomes]
rs1604700	1.00[EUR][1000 genomes]
rs1897238	1.00[EUR][1000 genomes]
rs2033390	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2567037	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2735557	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241549	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241550	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4287925	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4404474	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4443201	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4513473	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4515075	1.00[EUR][1000 genomes]
rs4616669	1.00[EUR][1000 genomes]
rs4858927	1.00[EUR][1000 genomes]
rs4858933	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4858970	1.00[EUR][1000 genomes]
rs4858987	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4858988	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4858989	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551270	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7615309	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7621357	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7625641	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7633215	0.88[ASN][1000 genomes]
rs7633486	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7636845	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7650749	1.00[EUR][1000 genomes]
rs7650912	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7650915	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs930154	1.00[EUR][1000 genomes]
rs9310062	1.00[EUR][1000 genomes]
rs9310063	1.00[EUR][1000 genomes]
rs9310064	0.89[AFR][1000 genomes]
rs9310069	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310073	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9812903	1.00[EUR][1000 genomes]
rs9833231	1.00[EUR][1000 genomes]
rs9850550	1.00[EUR][1000 genomes]
rs9860113	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9864564	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867614	1.00[EUR][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

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88109400-88115000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:88109400-88115000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:88109400-88115400	Weak transcription	Lung	lung
4	chr3:88109400-88124400	Weak transcription	Pancreas	Pancrea
5	chr3:88109800-88115000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr3:88109800-88115400	Weak transcription	Fetal Intestine Small	intestine
7	chr3:88110000-88116600	Weak transcription	Thymus	Thymus
8	chr3:88110000-88118600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:88110000-88120400	Weak transcription	Fetal Stomach	stomach
10	chr3:88110000-88120400	Weak transcription	Fetal Thymus	thymus
11	chr3:88110000-88121000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr3:88110200-88115600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:88110200-88117200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:88110200-88124200	Weak transcription	Fetal Kidney	kidney
15	chr3:88110400-88120200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:88111200-88115400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:88111200-88117800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:88111400-88115600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr3:88111400-88116400	Weak transcription	Right Ventricle	heart
20	chr3:88111400-88117200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:88111400-88121600	Weak transcription	Fetal Brain Male	brain
22	chr3:88111400-88124200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:88111400-88133600	Weak transcription	Brain Angular Gyrus	brain
24	chr3:88111400-88136200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:88111400-88136200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:88111600-88114800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:88111600-88115800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:88111600-88116400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:88111600-88116800	Weak transcription	Primary B cells from cord blood	blood
30	chr3:88111600-88116800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr3:88111600-88118000	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr3:88111600-88119800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:88111600-88121200	Weak transcription	NHLF	lung
34	chr3:88111600-88123200	Weak transcription	Liver	Liver
35	chr3:88111600-88124000	Weak transcription	Right Atrium	heart
36	chr3:88111600-88124000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr3:88111600-88124000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:88111600-88124200	Weak transcription	Fetal Lung	lung
39	chr3:88111600-88135200	Weak transcription	HSMM	muscle
40	chr3:88111600-88135400	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr3:88111600-88135600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr3:88111800-88114400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:88111800-88123600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:88111800-88135400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:88112000-88115800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr3:88112200-88136600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:88112200-88154200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr3:88112400-88116400	Weak transcription	Aorta	Aorta
49	chr3:88112400-88117200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:88112400-88117200	Weak transcription	Fetal Heart	heart

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