Variant report

Variant	rs56088529
Chromosome Location	chr3:142146369-142146370
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142142395..142144953-chr3:142145162..142147972,2	MCF-7	breast:
2	chr3:142145296..142147116-chr3:142150982..142153061,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114127	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10935464	0.83[ASN][1000 genomes]
rs11707154	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11708870	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11709758	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11711164	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11711179	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11714244	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714528	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719737	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11720007	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2229032	0.83[ASN][1000 genomes]
rs2291363	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2306700	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3922731	0.80[ASN][1000 genomes]
rs55687115	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56370391	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6769123	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6777420	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6780665	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73238130	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73238131	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73238136	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73238138	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73238140	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73238143	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73238144	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73238145	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73238148	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73238150	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73238152	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73238155	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73238158	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73238159	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73238161	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73238169	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73238170	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73238173	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73238176	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73238185	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238186	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238195	0.80[ASN][1000 genomes]
rs73238201	0.80[ASN][1000 genomes]
rs73238202	0.80[ASN][1000 genomes]
rs7623513	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7633870	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642634	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv522549	chr3:141812759-142164735	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv523945	chr3:141933649-142219542	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv1000083	chr3:141956718-142172666	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv877557	chr3:142090402-142150204	Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv523596	chr3:142132749-142164735	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142083600-142158600	Weak transcription	NHEK	skin
2	chr3:142105000-142151800	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr3:142106800-142150800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:142112200-142151600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:142112200-142152000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr3:142112200-142152200	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr3:142112200-142154600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr3:142112400-142146600	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:142112600-142150600	Strong transcription	Placenta	Placenta
10	chr3:142113000-142152200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr3:142113400-142151800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:142113400-142151800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:142114800-142151800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:142120400-142151800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr3:142120600-142151800	Strong transcription	Dnd41	blood
16	chr3:142125000-142151800	Strong transcription	Fetal Thymus	thymus
17	chr3:142126000-142148600	Weak transcription	Fetal Brain Male	brain
18	chr3:142127000-142152000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:142127200-142149200	Weak transcription	Gastric	stomach
20	chr3:142127200-142152200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:142127400-142148400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:142127400-142159600	Weak transcription	Psoas Muscle	Psoas
23	chr3:142127800-142149400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:142129800-142148800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:142131400-142149200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:142131600-142156000	Weak transcription	Fetal Heart	heart
27	chr3:142132800-142148600	Weak transcription	NHLF	lung
28	chr3:142134200-142152600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr3:142136400-142157400	Weak transcription	HMEC	breast
30	chr3:142136800-142150800	Strong transcription	Liver	Liver
31	chr3:142138000-142147600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:142138200-142148800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr3:142138200-142148800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:142138400-142148200	Weak transcription	Brain Hippocampus Middle	brain
35	chr3:142138400-142149400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr3:142138600-142148600	Weak transcription	Aorta	Aorta
37	chr3:142138600-142148600	Weak transcription	Fetal Kidney	kidney
38	chr3:142138600-142158600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:142138600-142164600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:142138800-142146800	Weak transcription	Fetal Brain Female	brain
41	chr3:142138800-142148400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:142138800-142163000	Weak transcription	Spleen	Spleen
43	chr3:142139200-142148200	Weak transcription	Lung	lung
44	chr3:142139200-142151200	Weak transcription	Right Ventricle	heart
45	chr3:142139400-142148400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:142139400-142156200	Weak transcription	Small Intestine	intestine
47	chr3:142139400-142157000	Weak transcription	Brain Germinal Matrix	brain
48	chr3:142139400-142158600	Weak transcription	Pancreas	Pancrea
49	chr3:142139400-142163200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:142139600-142150400	Strong transcription	Primary hematopoietic stem cells	blood

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