Variant report

Variant	rs4413291
Chromosome Location	chr3:111431591-111431592
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	FOS	chr3:111431189-111431670	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr3:111431272-111431647	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr3:111431297-111431623	MCF10A-Er-Src	breast:	n/a	n/a
4	E2F4	chr3:111431393-111431610	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr3:111431188-111431603	MCF10A-Er-Src	breast:	n/a	chr3:111431389-111431397 chr3:111431292-111431304
6	MYC	chr3:111431445-111431636	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr3:111431160-111431740	U87	brain:	n/a	n/a
8	FOS	chr3:111431191-111431671	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr3:111431280-111431611	MCF10A-Er-Src	breast:	n/a	chr3:111431389-111431397 chr3:111431292-111431304
10	POLR2A	chr3:111431159-111431646	U87	brain:	n/a	n/a

Variant related genes	Relation type
PLCXD2	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10470303	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs11710738	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs11711533	0.92[CEU][hapmap];0.82[CHB][hapmap];0.82[YRI][hapmap]
rs11711582	1.00[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs12330761	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs12490166	0.89[GIH][hapmap]
rs13074817	0.89[GIH][hapmap]
rs13079085	0.89[GIH][hapmap]
rs2137595	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292518	0.82[JPT][hapmap]
rs4284954	0.89[GIH][hapmap]
rs4401340	0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs4431081	0.89[GIH][hapmap]
rs4682054	0.86[JPT][hapmap];0.85[MKK][hapmap]
rs4682057	0.88[EUR][1000 genomes]
rs4682298	0.91[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4682299	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.90[EUR][1000 genomes]
rs4682303	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs4682305	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs4682312	0.84[CEU][hapmap]
rs4682314	0.82[ASW][hapmap];0.84[CEU][hapmap]
rs56028731	0.89[EUR][1000 genomes]
rs62273780	0.82[EUR][1000 genomes]
rs62275532	0.89[EUR][1000 genomes]
rs6768713	0.89[GIH][hapmap]
rs6784753	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs6786612	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs6788543	0.92[CEU][hapmap];0.91[GIH][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs6796087	0.92[CEU][hapmap];0.91[GIH][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs7609653	0.87[EUR][1000 genomes]
rs955381	0.89[EUR][1000 genomes]
rs959540	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9818574	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs9823974	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs9834030	0.89[GIH][hapmap]
rs9868171	0.86[EUR][1000 genomes]
rs9868909	0.96[CEU][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs9870656	0.83[CEU][hapmap]
rs9877859	0.91[ASW][hapmap];1.00[YRI][hapmap]

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	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591290	chr3:111427455-111462570	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4413291	CCDC80	cis	parietal	SCAN
rs4413291	ZBED2	cis	parietal	SCAN
rs4413291	GAP43	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111410200-111433200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr3:111410600-111443400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:111415200-111454200	Weak transcription	Small Intestine	intestine
4	chr3:111415600-111436000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:111415600-111436400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:111418200-111442000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:111419000-111436000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:111419000-111436200	Weak transcription	Stomach Mucosa	stomach
9	chr3:111420400-111450600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:111420600-111445600	Weak transcription	HepG2	liver
11	chr3:111421400-111434600	Weak transcription	A549	lung
12	chr3:111422000-111433400	Weak transcription	HSMMtube	muscle
13	chr3:111423200-111434600	Weak transcription	HUVEC	blood vessel
14	chr3:111424600-111441800	Weak transcription	Thymus	Thymus
15	chr3:111425800-111441200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr3:111425800-111443800	Weak transcription	Dnd41	blood
17	chr3:111426800-111436400	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:111427000-111442400	Weak transcription	Ovary	ovary
19	chr3:111427200-111448400	Weak transcription	Right Ventricle	heart
20	chr3:111427400-111433200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:111427400-111434800	Weak transcription	Aorta	Aorta
22	chr3:111427600-111456000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr3:111428000-111432800	Weak transcription	Fetal Thymus	thymus
24	chr3:111428600-111433000	Weak transcription	Placenta	Placenta
25	chr3:111428800-111432800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:111428800-111434600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:111428800-111445200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:111428800-111451200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr3:111429000-111441000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr3:111429200-111433000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:111429400-111446800	Weak transcription	Fetal Intestine Large	intestine
32	chr3:111429600-111442400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:111429800-111432000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:111429800-111432600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr3:111430000-111432600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr3:111430200-111432000	Enhancers	Brain Germinal Matrix	brain
37	chr3:111430400-111432000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:111430400-111432000	Enhancers	Muscle Satellite Cultured Cells	--
39	chr3:111430400-111432000	Enhancers	NHEK	skin
40	chr3:111430600-111431800	Enhancers	Fetal Kidney	kidney
41	chr3:111430600-111433600	Strong transcription	Fetal Intestine Small	intestine
42	chr3:111430600-111435600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr3:111430600-111436600	Strong transcription	Primary T cells from cord blood	blood
44	chr3:111430800-111431800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:111430800-111431800	Enhancers	Fetal Brain Male	brain
46	chr3:111430800-111432000	Genic enhancers	Primary T cells fromperipheralblood	blood
47	chr3:111430800-111432000	Enhancers	HSMM	muscle
48	chr3:111430800-111432000	Enhancers	NHDF-Ad	bronchial
49	chr3:111430800-111432200	Enhancers	Osteobl	bone
50	chr3:111431000-111431600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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