Variant report

Variant	rs55699824
Chromosome Location	chr3:141690346-141690347
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10935449	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10935450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10935451	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10935454	0.80[EUR][1000 genomes]
rs11569177	0.80[EUR][1000 genomes]
rs11569186	0.80[EUR][1000 genomes]
rs11569193	0.82[EUR][1000 genomes]
rs11569195	0.82[EUR][1000 genomes]
rs11569202	0.80[EUR][1000 genomes]
rs11569205	0.82[EUR][1000 genomes]
rs11569206	0.82[EUR][1000 genomes]
rs11569209	0.80[EUR][1000 genomes]
rs11569214	0.82[EUR][1000 genomes]
rs11569218	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11569220	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11569222	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11569223	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11569226	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11569229	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11569232	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11569233	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11569234	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11569235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11569237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11569244	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11569246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11569247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11569248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11569249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11569251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11569252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11705778	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11706402	0.82[EUR][1000 genomes]
rs11708301	0.82[EUR][1000 genomes]
rs11711960	0.82[EUR][1000 genomes]
rs11712803	0.82[EUR][1000 genomes]
rs11714727	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11716148	0.80[EUR][1000 genomes]
rs11717517	0.82[EUR][1000 genomes]
rs11718167	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11719793	0.82[EUR][1000 genomes]
rs11720601	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12488739	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12488787	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12488810	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12493472	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12493495	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12493643	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34026748	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3828397	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4683415	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4683418	0.80[EUR][1000 genomes]
rs4683654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4683657	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4683659	0.80[EUR][1000 genomes]
rs56001234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56104495	0.80[EUR][1000 genomes]
rs56162837	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56184282	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61397493	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[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	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	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141629000-141739200	Weak transcription	Psoas Muscle	Psoas
2	chr3:141659200-141696200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:141660600-141698200	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr3:141666000-141697600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr3:141669600-141696800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:141671600-141697400	Weak transcription	Gastric	stomach
7	chr3:141671800-141691200	Weak transcription	Spleen	Spleen
8	chr3:141671800-141719000	Weak transcription	Placenta	Placenta
9	chr3:141671800-141724000	Weak transcription	Right Ventricle	heart
10	chr3:141671800-141735600	Weak transcription	Aorta	Aorta
11	chr3:141672000-141697000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:141672000-141700000	Weak transcription	Small Intestine	intestine
13	chr3:141674400-141708000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:141674600-141700400	Weak transcription	Esophagus	oesophagus
15	chr3:141674600-141712600	Weak transcription	Fetal Brain Male	brain
16	chr3:141676200-141703800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:141677400-141696200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr3:141677800-141691200	Weak transcription	Brain Anterior Caudate	brain
19	chr3:141677800-141739000	Weak transcription	Left Ventricle	heart
20	chr3:141678800-141745600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr3:141679400-141690600	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:141679600-141697000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr3:141679800-141691400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:141680000-141690600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:141680000-141697800	Weak transcription	NH-A	brain
26	chr3:141680000-141711200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:141680000-141731200	Weak transcription	Fetal Brain Female	brain
28	chr3:141680200-141697600	Weak transcription	Osteobl	bone
29	chr3:141680400-141697600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:141680800-141691000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:141680800-141723200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:141682000-141696600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr3:141682000-141711200	Weak transcription	GM12878-XiMat	blood
34	chr3:141682600-141690400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:141682600-141691000	Weak transcription	HMEC	breast
36	chr3:141682600-141691400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:141682600-141723400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:141682800-141692200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:141682800-141695000	Weak transcription	Adipose Nuclei	Adipose
40	chr3:141682800-141695200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:141682800-141695400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:141682800-141695400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:141682800-141696800	Weak transcription	Brain Hippocampus Middle	brain
44	chr3:141682800-141697800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:141682800-141698200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:141682800-141698800	Weak transcription	Brain Angular Gyrus	brain
47	chr3:141682800-141712200	Weak transcription	Ovary	ovary
48	chr3:141682800-141724600	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr3:141682800-141739000	Weak transcription	Pancreas	Pancrea
50	chr3:141682800-141745800	Weak transcription	Rectal Mucosa Donor 31	rectum

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