Variant report

Variant	rs11569229
Chromosome Location	chr3:141694858-141694859
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10935449	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10935450	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10935451	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11569218	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11569220	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11569222	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11569223	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11569226	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11569232	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11569233	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11569234	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11569235	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11569237	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11569244	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11569246	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11569247	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11569248	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11569249	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11569251	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11569252	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11705778	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11714727	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11718167	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11720601	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12488739	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12488787	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12488810	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12493472	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12493495	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12493643	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34026748	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3828397	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4683415	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4683654	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4683655	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4683656	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4683657	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55699824	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55920121	0.83[ASN][1000 genomes]
rs56001234	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56162837	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56184282	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61397493	0.89[EUR][1000 genomes];0.84[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11569229	TFDP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 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	chr3:141671800-141719000	Weak transcription	Placenta	Placenta
8	chr3:141671800-141724000	Weak transcription	Right Ventricle	heart
9	chr3:141671800-141735600	Weak transcription	Aorta	Aorta
10	chr3:141672000-141697000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:141672000-141700000	Weak transcription	Small Intestine	intestine
12	chr3:141674400-141708000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr3:141674600-141700400	Weak transcription	Esophagus	oesophagus
14	chr3:141674600-141712600	Weak transcription	Fetal Brain Male	brain
15	chr3:141676200-141703800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:141677400-141696200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr3:141677800-141739000	Weak transcription	Left Ventricle	heart
18	chr3:141678800-141745600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr3:141679600-141697000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:141680000-141697800	Weak transcription	NH-A	brain
21	chr3:141680000-141711200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:141680000-141731200	Weak transcription	Fetal Brain Female	brain
23	chr3:141680200-141697600	Weak transcription	Osteobl	bone
24	chr3:141680400-141697600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:141680800-141723200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:141682000-141696600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:141682000-141711200	Weak transcription	GM12878-XiMat	blood
28	chr3:141682600-141723400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:141682800-141695000	Weak transcription	Adipose Nuclei	Adipose
30	chr3:141682800-141695200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:141682800-141695400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:141682800-141695400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:141682800-141696800	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:141682800-141697800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:141682800-141698200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:141682800-141698800	Weak transcription	Brain Angular Gyrus	brain
37	chr3:141682800-141712200	Weak transcription	Ovary	ovary
38	chr3:141682800-141724600	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr3:141682800-141739000	Weak transcription	Pancreas	Pancrea
40	chr3:141682800-141745800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr3:141682800-141746200	Weak transcription	Primary B cells from peripheral blood	blood
42	chr3:141683000-141695200	Weak transcription	Liver	Liver
43	chr3:141683000-141719400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:141683200-141695200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:141683200-141697800	Weak transcription	HSMMtube	muscle
46	chr3:141683200-141709800	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr3:141683600-141716200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr3:141683800-141698600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:141683800-141704600	Weak transcription	Brain Germinal Matrix	brain
50	chr3:141683800-141746600	Weak transcription	Lung	lung

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