Variant report

Variant	rs4245741
Chromosome Location	chr1:211813029-211813030
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	STAT3	chr1:211812782-211813486	MCF10A-Er-Src	breast:	n/a	n/a
2	JUND	chr1:211812704-211813688	SK-N-SH	brain:	n/a	n/a
3	FOSL2	chr1:211812801-211813221	HepG2	liver:	n/a	n/a
4	EP300	chr1:211812726-211813814	SK-N-SH	brain:	n/a	chr1:211812943-211812953
5	GATA3	chr1:211812665-211813937	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr1:211812815-211813220	HUVEC	blood vessel:	n/a	n/a
7	TEAD4	chr1:211812781-211813706	SK-N-SH	brain:	n/a	n/a
8	MAX	chr1:211812816-211813728	Hela-S3	cervix:	n/a	n/a
9	FOS	chr1:211812777-211813452	MCF10A-Er-Src	breast:	n/a	n/a
10	MAFK	chr1:211812985-211813054	HepG2	liver:	n/a	n/a
11	BRCA1	chr1:211812819-211813935	Hela-S3	cervix:	n/a	n/a
12	FOS	chr1:211812775-211813799	MCF10A-Er-Src	breast:	n/a	n/a
13	TFAP2C	chr1:211811691-211813538	Hela-S3	cervix:	n/a	n/a
14	GTF3C2	chr1:211811970-211813137	Hela-S3	cervix:	n/a	n/a
15	CEBPB	chr1:211811877-211813893	Hela-S3	cervix:	n/a	n/a
16	USF2	chr1:211812736-211813650	Hela-S3	cervix:	n/a	n/a
17	RXRA	chr1:211812743-211813620	SK-N-SH	brain:	n/a	n/a
18	FOS	chr1:211812750-211813505	MCF10A-Er-Src	breast:	n/a	n/a
19	PBX3	chr1:211812758-211813716	SK-N-SH	brain:	n/a	n/a
20	JUND	chr1:211812796-211813728	Hela-S3	cervix:	n/a	n/a
21	JUN	chr1:211812808-211813434	HUVEC	blood vessel:	n/a	n/a
22	JUN	chr1:211812767-211814123	Hela-S3	cervix:	n/a	n/a
23	EP300	chr1:211812783-211813785	Hela-S3	cervix:	n/a	chr1:211812943-211812953
24	TBP	chr1:211812799-211813975	Hela-S3	cervix:	n/a	n/a
25	STAT3	chr1:211812798-211813243	MCF10A-Er-Src	breast:	n/a	n/a
26	RFX5	chr1:211812914-211813061	HepG2	liver:	n/a	chr1:211812995-211813010
27	POLR2A	chr1:211812662-211813953	Hela-S3	cervix:	n/a	n/a
28	MAX	chr1:211812774-211813623	SK-N-SH	brain:	n/a	n/a
29	RPC155	chr1:211812253-211813044	Hela-S3	cervix:	n/a	n/a
30	TAF1	chr1:211812732-211813620	Hela-S3	cervix:	n/a	n/a
31	FOSL2	chr1:211812843-211813152	A549	lung:	n/a	n/a
32	FOSL2	chr1:211812773-211813537	SK-N-SH	brain:	n/a	n/a
33	MAX	chr1:211812766-211813638	SK-N-SH	brain:	n/a	n/a
34	STAT3	chr1:211812741-211813490	MCF10A-Er-Src	breast:	n/a	n/a
35	TAF1	chr1:211812835-211813109	SK-N-SH	brain:	n/a	n/a
36	MYC	chr1:211812822-211813789	Hela-S3	cervix:	n/a	n/a
37	SMARCC1	chr1:211812818-211813827	Hela-S3	cervix:	n/a	n/a
38	CEBPB	chr1:211812863-211813645	IMR90	lung:	n/a	n/a
39	POLR2A	chr1:211812803-211813842	Hela-S3	cervix:	n/a	n/a
40	EP300	chr1:211812785-211813583	SK-N-SH	brain:	n/a	chr1:211812943-211812953
41	TCF12	chr1:211812751-211813737	SK-N-SH	brain:	n/a	n/a
42	YY1	chr1:211812734-211813525	SK-N-SH	brain:	n/a	n/a
43	RFX5	chr1:211811963-211813884	Hela-S3	cervix:	n/a	chr1:211812995-211813010
44	GTF2F1	chr1:211812762-211813833	Hela-S3	cervix:	n/a	n/a
45	FOS	chr1:211812787-211813419	MCF10A-Er-Src	breast:	n/a	n/a
46	TCF7L2	chr1:211811803-211813778	Hela-S3	cervix:	n/a	chr1:211812465-211812474
47	POLR2A	chr1:211812808-211813635	Hela-S3	cervix:	n/a	n/a
48	JUND	chr1:211812735-211813830	SK-N-SH	brain:	n/a	n/a
49	GATA3	chr1:211812736-211813915	SK-N-SH	brain:	n/a	n/a
50	MYC	chr1:211812782-211813463	MCF10A-Er-Src	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRAF5-5	chr1:211813005-211813231	NONHSAT009306

Variant related genes	Relation type
ENSG00000227764	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10158305	0.86[EUR][1000 genomes]
rs10158307	0.86[EUR][1000 genomes]
rs10158309	0.86[EUR][1000 genomes]
rs10158749	0.85[EUR][1000 genomes]
rs10158790	0.86[EUR][1000 genomes]
rs10158874	0.85[EUR][1000 genomes]
rs10159253	0.84[EUR][1000 genomes]
rs10779564	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10779565	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10779566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863919	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863920	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119780	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11119783	0.82[EUR][1000 genomes]
rs11119786	0.83[EUR][1000 genomes]
rs11119787	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11576789	0.81[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs11577255	0.83[EUR][1000 genomes]
rs12087826	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs12090722	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12123429	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12142250	0.85[EUR][1000 genomes]
rs12727505	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12741252	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12758005	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs1373293	0.86[EUR][1000 genomes]
rs35531215	0.84[EUR][1000 genomes]
rs4951415	0.88[ASN][1000 genomes]
rs4951416	0.91[CEU][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951418	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951419	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951421	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951537	0.82[ASN][1000 genomes]
rs4951539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951540	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61851777	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6540697	0.87[MEX][hapmap]
rs6540698	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6660850	0.87[MEX][hapmap]
rs6669878	0.86[EUR][1000 genomes]
rs6670986	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6671497	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6671506	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6675796	0.83[CEU][hapmap]
rs6682640	0.82[AMR][1000 genomes]
rs6693364	0.82[EUR][1000 genomes]
rs7513348	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7523748	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7527270	1.00[CHB][hapmap]
rs7551699	0.83[EUR][1000 genomes]
rs894853	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs894854	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs894855	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010919	chr1:211804252-211823073	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4245741	PLXNA2	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211804200-211813400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:211804200-211816600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:211807000-211816200	Weak transcription	Colonic Mucosa	Colon
4	chr1:211807000-211816200	Weak transcription	Ovary	ovary
5	chr1:211807200-211816600	Weak transcription	Right Ventricle	heart
6	chr1:211807200-211817200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:211807400-211816800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:211807600-211816600	Weak transcription	Left Ventricle	heart
9	chr1:211810600-211816400	Weak transcription	Spleen	Spleen
10	chr1:211811200-211813600	Enhancers	Placenta	Placenta
11	chr1:211811400-211829600	Enhancers	Fetal Intestine Small	intestine
12	chr1:211811600-211815000	Enhancers	Liver	Liver
13	chr1:211811600-211828200	Enhancers	Fetal Intestine Large	intestine
14	chr1:211811800-211814000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:211812000-211813200	Enhancers	Muscle Satellite Cultured Cells	--
16	chr1:211812000-211813200	Enhancers	HMEC	breast
17	chr1:211812000-211813800	Enhancers	NHDF-Ad	bronchial
18	chr1:211812000-211814000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:211812000-211814400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:211812200-211813400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:211812400-211816600	Weak transcription	Adipose Nuclei	Adipose
22	chr1:211812600-211816600	Weak transcription	Esophagus	oesophagus
23	chr1:211812800-211813200	Enhancers	Pancreas	Pancrea
24	chr1:211812800-211814000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr1:211813000-211813200	Enhancers	Gastric	stomach
26	chr1:211813000-211813400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:211813000-211813400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:211813000-211813400	Enhancers	Aorta	Aorta
29	chr1:211813000-211813400	Enhancers	HSMMtube	muscle
30	chr1:211813000-211813400	Active TSS	NHLF	lung
31	chr1:211813000-211813600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:211813000-211813600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:211813000-211813600	Flanking Active TSS	HepG2	liver
34	chr1:211813000-211813600	Enhancers	HSMM	muscle
35	chr1:211813000-211813800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:211813000-211813800	Enhancers	Stomach Mucosa	stomach
37	chr1:211813000-211813800	Flanking Active TSS	A549	lung
38	chr1:211813000-211813800	Flanking Active TSS	Osteobl	bone
39	chr1:211813000-211814000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:211813000-211814000	Flanking Active TSS	HUVEC	blood vessel
41	chr1:211813000-211814000	Flanking Active TSS	NH-A	brain
42	chr1:211813000-211814600	Active TSS	Hela-S3	cervix

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