Variant report

Variant	rs11569206
Chromosome Location	chr3:141713286-141713287
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10935446	1.00[CEU][hapmap]
rs10935449	0.89[EUR][1000 genomes]
rs10935450	0.89[EUR][1000 genomes]
rs10935451	0.89[EUR][1000 genomes]
rs10935454	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11569177	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11569186	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11569190	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11569193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11569195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11569201	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11569202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11569205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11569208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11569209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11569214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11569218	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11569220	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11569222	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11569223	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11569226	0.89[EUR][1000 genomes]
rs11569232	0.85[EUR][1000 genomes]
rs11569233	0.85[EUR][1000 genomes]
rs11569234	0.85[EUR][1000 genomes]
rs11569235	0.84[EUR][1000 genomes]
rs11569237	0.85[EUR][1000 genomes]
rs11569244	0.85[EUR][1000 genomes]
rs11569246	0.85[EUR][1000 genomes]
rs11569247	0.85[EUR][1000 genomes]
rs11569248	0.85[EUR][1000 genomes]
rs11569249	0.85[EUR][1000 genomes]
rs11569251	0.85[EUR][1000 genomes]
rs11569252	0.85[EUR][1000 genomes]
rs11569278	1.00[CEU][hapmap]
rs11569291	1.00[CEU][hapmap]
rs11705778	0.89[EUR][1000 genomes]
rs11706402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11706728	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11708301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11711748	1.00[CEU][hapmap]
rs11711960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11712803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11713023	1.00[CEU][hapmap]
rs11713062	0.84[ASN][1000 genomes]
rs11713690	0.88[ASN][1000 genomes]
rs11714727	0.85[EUR][1000 genomes]
rs11716148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11717306	0.84[ASN][1000 genomes]
rs11717517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11718167	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11719793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11719806	0.84[ASN][1000 genomes]
rs11720300	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs11720601	0.89[EUR][1000 genomes]
rs12488739	0.85[EUR][1000 genomes]
rs12488787	0.89[EUR][1000 genomes]
rs12488810	0.89[EUR][1000 genomes]
rs12493472	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12493495	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12493643	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12494971	1.00[CEU][hapmap]
rs34026748	0.89[EUR][1000 genomes]
rs34262349	0.84[ASN][1000 genomes]
rs3828397	0.85[EUR][1000 genomes]
rs4683413	1.00[CEU][hapmap]
rs4683415	0.89[EUR][1000 genomes]
rs4683418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4683419	0.84[ASN][1000 genomes]
rs4683654	0.85[EUR][1000 genomes]
rs4683655	0.85[EUR][1000 genomes]
rs4683656	0.89[EUR][1000 genomes]
rs4683657	0.89[EUR][1000 genomes]
rs4683659	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4683660	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4683661	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4683665	0.84[ASN][1000 genomes]
rs4683669	1.00[CHB][hapmap]
rs55644127	0.88[ASN][1000 genomes]
rs55680729	0.84[ASN][1000 genomes]
rs55699824	0.82[EUR][1000 genomes]
rs55778028	0.88[ASN][1000 genomes]
rs55787733	0.84[ASN][1000 genomes]
rs55871523	0.84[ASN][1000 genomes]
rs55959014	0.84[ASN][1000 genomes]
rs56001234	0.85[EUR][1000 genomes]
rs56104495	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56116145	0.84[ASN][1000 genomes]
rs56128490	0.84[ASN][1000 genomes]
rs56162837	0.89[EUR][1000 genomes]
rs56184282	0.89[EUR][1000 genomes]
rs56200713	0.84[ASN][1000 genomes]
rs56300836	0.84[ASN][1000 genomes]
rs56324837	0.84[ASN][1000 genomes]
rs61397493	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs61729566	0.88[ASN][1000 genomes]
rs61737218	0.88[ASN][1000 genomes]
rs73232653	0.84[ASN][1000 genomes]
rs73232654	0.84[ASN][1000 genomes]
rs73232657	0.84[ASN][1000 genomes]
rs73232659	0.84[ASN][1000 genomes]
rs73232663	0.84[ASN][1000 genomes]
rs73232664	0.84[ASN][1000 genomes]
rs73232666	0.84[ASN][1000 genomes]
rs73232667	0.84[ASN][1000 genomes]
rs73232670	0.84[ASN][1000 genomes]
rs73232672	0.84[ASN][1000 genomes]
rs73232673	0.84[ASN][1000 genomes]
rs73232675	0.84[ASN][1000 genomes]
rs73232677	0.84[ASN][1000 genomes]
rs73232678	0.84[ASN][1000 genomes]
rs73232684	0.84[ASN][1000 genomes]
rs73232685	0.84[ASN][1000 genomes]
rs73232693	0.84[ASN][1000 genomes]
rs73232695	0.84[ASN][1000 genomes]
rs73233851	0.84[ASN][1000 genomes]
rs73233852	0.84[ASN][1000 genomes]
rs73233853	0.84[ASN][1000 genomes]
rs9868050	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][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
rs11569206	TFDP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141629000-141739200	Weak transcription	Psoas Muscle	Psoas
2	chr3:141671800-141719000	Weak transcription	Placenta	Placenta
3	chr3:141671800-141724000	Weak transcription	Right Ventricle	heart
4	chr3:141671800-141735600	Weak transcription	Aorta	Aorta
5	chr3:141677800-141739000	Weak transcription	Left Ventricle	heart
6	chr3:141678800-141745600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:141680000-141731200	Weak transcription	Fetal Brain Female	brain
8	chr3:141680800-141723200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:141682600-141723400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:141682800-141724600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr3:141682800-141739000	Weak transcription	Pancreas	Pancrea
12	chr3:141682800-141745800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:141682800-141746200	Weak transcription	Primary B cells from peripheral blood	blood
14	chr3:141683000-141719400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:141683600-141716200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr3:141683800-141746600	Weak transcription	Lung	lung
17	chr3:141688000-141719400	Strong transcription	Dnd41	blood
18	chr3:141688400-141714600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:141688800-141720200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:141688800-141729000	Strong transcription	Fetal Thymus	thymus
21	chr3:141689400-141720000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:141691800-141722800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:141696400-141719600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:141697200-141718800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:141697400-141727200	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:141697600-141719000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr3:141697600-141719000	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:141697600-141725800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:141697800-141719200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:141698400-141715000	Weak transcription	NH-A	brain
31	chr3:141698400-141715200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:141698400-141715200	Weak transcription	HSMMtube	muscle
33	chr3:141698400-141715400	Weak transcription	NHDF-Ad	bronchial
34	chr3:141698400-141721400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:141698600-141738800	Weak transcription	HSMM	muscle
36	chr3:141699800-141715400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:141704000-141716200	Weak transcription	Fetal Heart	heart
38	chr3:141704200-141725400	Weak transcription	Spleen	Spleen
39	chr3:141705000-141714400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:141705600-141715400	Weak transcription	Brain Germinal Matrix	brain
41	chr3:141706000-141714200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:141706400-141746200	Weak transcription	Fetal Lung	lung
43	chr3:141706800-141713600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr3:141706800-141714400	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:141707200-141714000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:141707200-141734400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:141708400-141731200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:141708600-141728400	Weak transcription	Liver	Liver
49	chr3:141708600-141745200	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr3:141709000-141719600	Weak transcription	Fetal Stomach	stomach

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