Variant report

Variant	rs11569190
Chromosome Location	chr3:141722754-141722755
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr3:141722704-141723419	SK-N-SH	brain:	n/a	n/a
2	EP300	chr3:141722697-141723368	T-47D	breast:	n/a	n/a

Variant related genes	Relation type
TFDP2	TF binding region

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10935446	1.00[CEU][hapmap]
rs10935454	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11569177	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11569186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11569193	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11569195	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11569201	1.00[CEU][hapmap];0.95[ASN][1000 genomes]
rs11569202	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11569205	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11569206	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11569208	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11569209	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11569214	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11569218	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap]
rs11569220	1.00[CEU][hapmap]
rs11569222	1.00[CEU][hapmap]
rs11569223	1.00[CEU][hapmap]
rs11569278	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap]
rs11569291	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap]
rs11706402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11706728	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11708301	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11711748	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap]
rs11711960	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11712803	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11713023	1.00[CEU][hapmap]
rs11713062	0.87[ASN][1000 genomes]
rs11713690	0.91[ASN][1000 genomes]
rs11716148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11717306	0.87[ASN][1000 genomes]
rs11717517	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11718167	1.00[CEU][hapmap]
rs11719793	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11719806	0.87[ASN][1000 genomes]
rs11720300	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs12493472	1.00[CEU][hapmap]
rs12493495	1.00[CEU][hapmap]
rs12493643	1.00[CEU][hapmap]
rs12494971	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap]
rs34262349	0.87[ASN][1000 genomes]
rs4683413	1.00[CEU][hapmap]
rs4683418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683419	0.87[ASN][1000 genomes]
rs4683659	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683660	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4683661	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4683665	0.87[ASN][1000 genomes]
rs4683669	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap]
rs55644127	0.91[ASN][1000 genomes]
rs55680729	0.87[ASN][1000 genomes]
rs55778028	0.91[ASN][1000 genomes]
rs55787733	0.87[ASN][1000 genomes]
rs55871523	0.87[ASN][1000 genomes]
rs55959014	0.87[ASN][1000 genomes]
rs56104495	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56116145	0.87[ASN][1000 genomes]
rs56128490	0.87[ASN][1000 genomes]
rs56200713	0.87[ASN][1000 genomes]
rs56300836	0.87[ASN][1000 genomes]
rs56324837	0.87[ASN][1000 genomes]
rs61729566	0.91[ASN][1000 genomes]
rs61737218	0.91[ASN][1000 genomes]
rs73232653	0.87[ASN][1000 genomes]
rs73232654	0.87[ASN][1000 genomes]
rs73232657	0.87[ASN][1000 genomes]
rs73232659	0.87[ASN][1000 genomes]
rs73232663	0.87[ASN][1000 genomes]
rs73232664	0.87[ASN][1000 genomes]
rs73232666	0.87[ASN][1000 genomes]
rs73232667	0.87[ASN][1000 genomes]
rs73232670	0.87[ASN][1000 genomes]
rs73232672	0.87[ASN][1000 genomes]
rs73232673	0.87[ASN][1000 genomes]
rs73232675	0.87[ASN][1000 genomes]
rs73232677	0.87[ASN][1000 genomes]
rs73232678	0.87[ASN][1000 genomes]
rs73232684	0.87[ASN][1000 genomes]
rs73232685	0.87[ASN][1000 genomes]
rs73232688	0.83[ASN][1000 genomes]
rs73232693	0.87[ASN][1000 genomes]
rs73232695	0.87[ASN][1000 genomes]
rs73233851	0.87[ASN][1000 genomes]
rs73233852	0.87[ASN][1000 genomes]
rs73233853	0.87[ASN][1000 genomes]
rs9868050	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv1002446	chr3:141719169-142070290	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11569190	TFDP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141629000-141739200	Weak transcription	Psoas Muscle	Psoas
2	chr3:141671800-141724000	Weak transcription	Right Ventricle	heart
3	chr3:141671800-141735600	Weak transcription	Aorta	Aorta
4	chr3:141677800-141739000	Weak transcription	Left Ventricle	heart
5	chr3:141678800-141745600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:141680000-141731200	Weak transcription	Fetal Brain Female	brain
7	chr3:141680800-141723200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:141682600-141723400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:141682800-141724600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr3:141682800-141739000	Weak transcription	Pancreas	Pancrea
11	chr3:141682800-141745800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:141682800-141746200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr3:141683800-141746600	Weak transcription	Lung	lung
14	chr3:141688800-141729000	Strong transcription	Fetal Thymus	thymus
15	chr3:141691800-141722800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:141697400-141727200	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr3:141697600-141725800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:141698600-141738800	Weak transcription	HSMM	muscle
19	chr3:141704200-141725400	Weak transcription	Spleen	Spleen
20	chr3:141706400-141746200	Weak transcription	Fetal Lung	lung
21	chr3:141707200-141734400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:141708400-141731200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:141708600-141728400	Weak transcription	Liver	Liver
24	chr3:141708600-141745200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr3:141711800-141732400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr3:141713000-141724400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr3:141713200-141722800	Weak transcription	Primary B cells from cord blood	blood
28	chr3:141714200-141722800	Weak transcription	Adipose Nuclei	Adipose
29	chr3:141715800-141723200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:141716000-141723000	Weak transcription	HSMMtube	muscle
31	chr3:141716000-141724600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:141716000-141732400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:141716000-141738600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:141716000-141745600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr3:141716200-141722800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:141716600-141724000	Weak transcription	Ovary	ovary
37	chr3:141718600-141724200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:141719000-141724200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:141719600-141723000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:141719600-141724600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:141719600-141738600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:141719600-141738600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr3:141719600-141739000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:141719800-141728600	Strong transcription	Dnd41	blood
45	chr3:141720000-141724400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:141720200-141725800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr3:141720200-141738000	Weak transcription	Fetal Intestine Large	intestine
48	chr3:141720200-141746600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:141720400-141732400	Weak transcription	Fetal Stomach	stomach
50	chr3:141720400-141737400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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