Variant report

Variant	rs11569223
Chromosome Location	chr3:141697786-141697787
allele	C/T
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	JUND	chr3:141697720-141698316	HCT-116	colon:	n/a	n/a
2	FOSL1	chr3:141697756-141698319	HCT-116	colon:	n/a	n/a
3	POLR2A	chr3:141697676-141698246	K562	blood:	n/a	n/a
4	STAT3	chr3:141697683-141698107	MCF10A-Er-Src	breast:	n/a	n/a
5	EP300	chr3:141697372-141698488	T-47D	breast:	n/a	n/a
6	FOSL1	chr3:141697738-141698384	HCT-116	colon:	n/a	n/a
7	FOXA1	chr3:141697598-141698350	T-47D	breast:	n/a	chr3:141697790-141697805
8	ATF3	chr3:141697780-141698240	HCT-116	colon:	n/a	n/a
9	JUND	chr3:141697769-141698281	T-47D	breast:	n/a	n/a
10	CEBPB	chr3:141697681-141698381	HCT-116	colon:	n/a	n/a
11	CBX3	chr3:141697760-141698241	HCT-116	colon:	n/a	n/a
12	CEBPB	chr3:141697773-141698292	HCT-116	colon:	n/a	n/a
13	USF1	chr3:141697782-141698283	HCT-116	colon:	n/a	n/a
14	SP1	chr3:141697741-141698313	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
TFDP2	TF binding region

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10935446	1.00[CEU][hapmap]
rs10935449	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10935450	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935454	0.87[EUR][1000 genomes]
rs11569177	0.87[EUR][1000 genomes]
rs11569186	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11569190	1.00[CEU][hapmap]
rs11569193	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11569195	0.89[EUR][1000 genomes]
rs11569201	1.00[CEU][hapmap]
rs11569202	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11569205	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11569206	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11569208	1.00[CEU][hapmap]
rs11569209	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11569214	0.89[EUR][1000 genomes]
rs11569218	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11569220	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11569222	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];1.00[ASN][1000 genomes]
rs11569226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11569229	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11569232	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11569233	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11569234	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11569235	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11569237	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11569244	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11569246	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11569247	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11569248	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11569249	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11569251	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11569252	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11569259	0.82[EUR][1000 genomes]
rs11569262	0.82[EUR][1000 genomes]
rs11569278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11569291	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11705778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706402	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11708301	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11711748	1.00[CEU][hapmap]
rs11711960	0.89[EUR][1000 genomes]
rs11712803	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11713023	1.00[CEU][hapmap]
rs11714727	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11716148	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11717517	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11718167	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];1.00[ASN][1000 genomes]
rs11719793	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11720601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493472	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12493495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493643	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12494971	1.00[CEU][hapmap]
rs34026748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828397	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4683414	0.82[EUR][1000 genomes]
rs4683415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683418	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4683654	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683655	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4683656	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683659	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs4683660	0.82[EUR][1000 genomes]
rs55699824	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55920121	0.84[ASN][1000 genomes]
rs56001234	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56104495	0.87[EUR][1000 genomes]
rs56162837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56184282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61397493	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637273	0.86[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
rs11569223	TFDP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141629000-141739200	Weak transcription	Psoas Muscle	Psoas
2	chr3:141660600-141698200	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr3:141671800-141719000	Weak transcription	Placenta	Placenta
4	chr3:141671800-141724000	Weak transcription	Right Ventricle	heart
5	chr3:141671800-141735600	Weak transcription	Aorta	Aorta
6	chr3:141672000-141700000	Weak transcription	Small Intestine	intestine
7	chr3:141674400-141708000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr3:141674600-141700400	Weak transcription	Esophagus	oesophagus
9	chr3:141674600-141712600	Weak transcription	Fetal Brain Male	brain
10	chr3:141676200-141703800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:141677800-141739000	Weak transcription	Left Ventricle	heart
12	chr3:141678800-141745600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr3:141680000-141697800	Weak transcription	NH-A	brain
14	chr3:141680000-141711200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:141680000-141731200	Weak transcription	Fetal Brain Female	brain
16	chr3:141680800-141723200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:141682000-141711200	Weak transcription	GM12878-XiMat	blood
18	chr3:141682600-141723400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:141682800-141697800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:141682800-141698200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:141682800-141698800	Weak transcription	Brain Angular Gyrus	brain
22	chr3:141682800-141712200	Weak transcription	Ovary	ovary
23	chr3:141682800-141724600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr3:141682800-141739000	Weak transcription	Pancreas	Pancrea
25	chr3:141682800-141745800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:141682800-141746200	Weak transcription	Primary B cells from peripheral blood	blood
27	chr3:141683000-141719400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:141683200-141697800	Weak transcription	HSMMtube	muscle
29	chr3:141683200-141709800	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr3:141683600-141716200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:141683800-141698600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:141683800-141704600	Weak transcription	Brain Germinal Matrix	brain
33	chr3:141683800-141746600	Weak transcription	Lung	lung
34	chr3:141686800-141700600	Weak transcription	HepG2	liver
35	chr3:141688000-141697800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:141688000-141702000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:141688000-141704800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:141688000-141719400	Strong transcription	Dnd41	blood
39	chr3:141688400-141698000	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr3:141688400-141698000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr3:141688400-141714600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:141688800-141706200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:141688800-141711200	Weak transcription	Fetal Kidney	kidney
44	chr3:141688800-141720200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:141688800-141729000	Strong transcription	Fetal Thymus	thymus
46	chr3:141689400-141698200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:141689400-141706800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:141689400-141720000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr3:141689600-141698200	Weak transcription	HSMM	muscle
50	chr3:141689600-141698800	Weak transcription	Primary T helper cells fromperipheralblood	blood

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