Variant report

Variant	rs11569220
Chromosome Location	chr3:141697980-141697981
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	MYC	chr3:141697889-141698390	MCF10A-Er-Src	breast:	n/a	n/a
2	SIN3AK20	chr3:141697867-141698191	HCT-116	colon:	n/a	n/a
3	JUND	chr3:141697720-141698316	HCT-116	colon:	n/a	n/a
4	ESR1	chr3:141697906-141698267	T-47D	breast:	n/a	n/a
5	FOSL1	chr3:141697756-141698319	HCT-116	colon:	n/a	n/a
6	POLR2A	chr3:141697874-141698177	MCF10A-Er-Src	breast:	n/a	n/a
7	CEBPB	chr3:141697846-141698206	IMR90	lung:	n/a	n/a
8	POLR2A	chr3:141697676-141698246	K562	blood:	n/a	n/a
9	GATA3	chr3:141697830-141698485	T-47D	breast:	n/a	chr3:141697857-141697866
10	STAT3	chr3:141697683-141698107	MCF10A-Er-Src	breast:	n/a	n/a
11	ATF3	chr3:141697817-141698302	HCT-116	colon:	n/a	n/a
12	JUN	chr3:141697890-141698208	HUVEC	blood vessel:	n/a	n/a
13	FOS	chr3:141697843-141698251	MCF10A-Er-Src	breast:	n/a	n/a
14	EP300	chr3:141697372-141698488	T-47D	breast:	n/a	n/a
15	FOSL1	chr3:141697738-141698384	HCT-116	colon:	n/a	n/a
16	FOS	chr3:141697801-141698311	MCF10A-Er-Src	breast:	n/a	n/a
17	MAX	chr3:141697953-141698178	Hela-S3	cervix:	n/a	n/a
18	CEBPB	chr3:141697843-141698202	Hela-S3	cervix:	n/a	n/a
19	JUND	chr3:141697820-141698277	HCT-116	colon:	n/a	n/a
20	FOSL2	chr3:141697885-141698323	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr3:141697936-141698146	HCT-116	colon:	n/a	n/a
22	FOXA1	chr3:141697598-141698350	T-47D	breast:	n/a	chr3:141697790-141697805
23	EP300	chr3:141697859-141698204	Hela-S3	cervix:	n/a	n/a
24	CEBPB	chr3:141697871-141698154	A549	lung:	n/a	n/a
25	GATA3	chr3:141697872-141698282	T-47D	breast:	n/a	n/a
26	SP1	chr3:141697826-141698229	HCT-116	colon:	n/a	n/a
27	STAT3	chr3:141697904-141698184	MCF10A-Er-Src	breast:	n/a	n/a
28	NFYB	chr3:141697849-141698106	Hela-S3	cervix:	n/a	chr3:141697962-141697977
29	ATF3	chr3:141697780-141698240	HCT-116	colon:	n/a	n/a
30	FOS	chr3:141697833-141698333	MCF10A-Er-Src	breast:	n/a	n/a
31	JUND	chr3:141697769-141698281	T-47D	breast:	n/a	n/a
32	MAFK	chr3:141697863-141698188	IMR90	lung:	n/a	n/a
33	CEBPB	chr3:141697681-141698381	HCT-116	colon:	n/a	n/a
34	FOXA1	chr3:141697915-141698227	T-47D	breast:	n/a	n/a
35	STAT3	chr3:141697816-141698439	MCF10A-Er-Src	breast:	n/a	n/a
36	CBX3	chr3:141697760-141698241	HCT-116	colon:	n/a	n/a
37	FOS	chr3:141697846-141698357	MCF10A-Er-Src	breast:	n/a	n/a
38	EP300	chr3:141697852-141698215	T-47D	breast:	n/a	n/a
39	CEBPB	chr3:141697773-141698292	HCT-116	colon:	n/a	n/a
40	USF1	chr3:141697782-141698283	HCT-116	colon:	n/a	n/a
41	MYC	chr3:141697906-141698281	MCF10A-Er-Src	breast:	n/a	n/a
42	SP1	chr3:141697741-141698313	HCT-116	colon:	n/a	n/a
43	STAT3	chr3:141697904-141698196	MCF10A-Er-Src	breast:	n/a	n/a
44	FOS	chr3:141697881-141698408	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
TFDP2	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10935446	1.00[CEU][hapmap]
rs10935449	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10935450	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10935451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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[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]
rs11569222	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]
rs11569223	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]
rs11569226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11569229	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11569232	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11569233	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11569234	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11569235	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11569237	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11569244	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11569246	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11569247	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11569248	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11569249	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11569251	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11569252	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11569259	0.82[EUR][1000 genomes]
rs11569262	0.82[EUR][1000 genomes]
rs11569278	1.00[CEU][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];0.95[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];1.00[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[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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];0.95[ASN][1000 genomes]
rs12488739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12488787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12488810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12493472	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]
rs12493495	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12493643	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]
rs12494971	1.00[CEU][hapmap]
rs34026748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3828397	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4683413	1.00[CEU][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];0.95[ASN][1000 genomes]
rs4683418	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4683654	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4683655	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4683656	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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];0.82[ASN][1000 genomes]
rs56001234	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[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];0.95[ASN][1000 genomes]
rs56184282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61397493	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7637273	0.81[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
rs11569220	TFDP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 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	chr3:141680000-141711200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:141680000-141731200	Weak transcription	Fetal Brain Female	brain
15	chr3:141680800-141723200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:141682000-141711200	Weak transcription	GM12878-XiMat	blood
17	chr3:141682600-141723400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:141682800-141698200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:141682800-141698800	Weak transcription	Brain Angular Gyrus	brain
20	chr3:141682800-141712200	Weak transcription	Ovary	ovary
21	chr3:141682800-141724600	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr3:141682800-141739000	Weak transcription	Pancreas	Pancrea
23	chr3:141682800-141745800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr3:141682800-141746200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr3:141683000-141719400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:141683200-141709800	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr3:141683600-141716200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr3:141683800-141698600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:141683800-141704600	Weak transcription	Brain Germinal Matrix	brain
30	chr3:141683800-141746600	Weak transcription	Lung	lung
31	chr3:141686800-141700600	Weak transcription	HepG2	liver
32	chr3:141688000-141702000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:141688000-141704800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:141688000-141719400	Strong transcription	Dnd41	blood
35	chr3:141688400-141698000	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:141688400-141698000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:141688400-141714600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:141688800-141706200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:141688800-141711200	Weak transcription	Fetal Kidney	kidney
40	chr3:141688800-141720200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr3:141688800-141729000	Strong transcription	Fetal Thymus	thymus
42	chr3:141689400-141698200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:141689400-141706800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr3:141689400-141720000	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr3:141689600-141698200	Weak transcription	HSMM	muscle
46	chr3:141689600-141698800	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr3:141689600-141698800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:141691400-141712200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:141691600-141700000	Weak transcription	HMEC	breast
50	chr3:141691600-141706000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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