Variant report

Variant	rs56781488
Chromosome Location	chr3:87034679-87034680
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10514743	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17028628	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1898266	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1898267	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1898268	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1946747	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55854261	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56077607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56338126	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56346369	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57070008	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57383190	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57543641	0.93[ASN][1000 genomes]
rs57604593	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59090592	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59701679	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61594756	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6551256	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763484	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802660	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72916057	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72916059	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72916062	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72916064	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72916069	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72916081	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72916083	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72916086	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72916091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72916092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72916098	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72916100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72916102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72918103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72918106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72918107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72918108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72918113	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72918116	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72918121	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72918124	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72918169	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73844420	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73844421	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73844432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73844434	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73844442	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73844457	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7617401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7627441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7645797	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649313	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs959081	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];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	nsv534036	chr3:86967129-87283600	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1000548	chr3:87034157-87331360	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:86998800-87036000	Weak transcription	Psoas Muscle	Psoas
2	chr3:87007200-87038400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr3:87016200-87039000	Weak transcription	Fetal Stomach	stomach
4	chr3:87016800-87036800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr3:87017600-87039000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:87018400-87036400	Weak transcription	Fetal Intestine Large	intestine
7	chr3:87019400-87036600	Weak transcription	Fetal Brain Male	brain
8	chr3:87028000-87035600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:87028000-87036200	Weak transcription	HMEC	breast
10	chr3:87030200-87036200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:87031600-87039600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:87032000-87034800	Enhancers	Colon Smooth Muscle	Colon
13	chr3:87032000-87037400	Enhancers	Rectal Smooth Muscle	rectum
14	chr3:87032400-87035400	Flanking Active TSS	NHDF-Ad	bronchial
15	chr3:87032400-87035600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:87032400-87035600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:87032400-87036000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:87032800-87039000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:87032800-87039200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:87033000-87036200	Weak transcription	Aorta	Aorta
21	chr3:87033000-87041000	Active TSS	Placenta	Placenta
22	chr3:87033400-87035200	Active TSS	NHLF	lung
23	chr3:87033600-87034800	Enhancers	A549	lung
24	chr3:87033600-87036000	Enhancers	Hela-S3	cervix
25	chr3:87033600-87036200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:87033800-87036000	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr3:87033800-87036200	Enhancers	Placenta Amnion	Placenta Amnion
28	chr3:87033800-87037400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr3:87033800-87041200	Active TSS	HSMMtube	muscle
30	chr3:87034000-87035000	Enhancers	Fetal Lung	lung
31	chr3:87034000-87035800	Enhancers	Adipose Nuclei	Adipose
32	chr3:87034200-87034800	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr3:87034200-87034800	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr3:87034200-87034800	Active TSS	Right Atrium	heart
35	chr3:87034200-87034800	Flanking Active TSS	HSMM	muscle
36	chr3:87034200-87035600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:87034400-87034800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:87034400-87034800	Flanking Active TSS	NH-A	brain
39	chr3:87034400-87035000	Active TSS	Ovary	ovary
40	chr3:87034600-87034800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:87034600-87034800	Active TSS	Fetal Muscle Leg	muscle
42	chr3:87034600-87035200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:87034600-87035400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:87034600-87035400	Transcr. at gene 5' and 3'	Osteobl	bone
45	chr3:87034600-87035800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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