Variant report

Variant	rs40705
Chromosome Location	chr5:9269246-9269247
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	GATA3	chr5:9269092-9269685	SH-SY5Y	brain:	n/a	n/a
2	EP300	chr5:9269171-9269575	SK-N-SH_RA	brain:	n/a	n/a
3	FOS	chr5:9269102-9269658	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr5:9269101-9269660	MCF10A-Er-Src	breast:	n/a	n/a
5	FOSL2	chr5:9269206-9269459	SK-N-SH	brain:	n/a	n/a
6	JUND	chr5:9269053-9269607	SK-N-SH	brain:	n/a	n/a
7	PBX3	chr5:9269104-9269565	SK-N-SH	brain:	n/a	n/a
8	FOSL2	chr5:9269025-9269585	SK-N-SH	brain:	n/a	n/a
9	MYC	chr5:9269211-9269611	MCF10A-Er-Src	breast:	n/a	n/a
10	GATA3	chr5:9268931-9269773	SK-N-SH	brain:	n/a	n/a
11	EP300	chr5:9269147-9269495	SK-N-SH_RA	brain:	n/a	n/a
12	GATA3	chr5:9268900-9269708	SK-N-SH	brain:	n/a	n/a
13	RAD21	chr5:9269154-9269521	SK-N-SH_RA	brain:	n/a	n/a
14	TCF12	chr5:9268999-9269751	SK-N-SH	brain:	n/a	n/a
15	GATA2	chr5:9269029-9269618	SH-SY5Y	brain:	n/a	n/a
16	TCF12	chr5:9269035-9269712	SK-N-SH	brain:	n/a	n/a
17	EP300	chr5:9268966-9269659	SK-N-SH	brain:	n/a	n/a
18	TEAD4	chr5:9269065-9269471	SK-N-SH	brain:	n/a	n/a
19	GATA3	chr5:9269112-9269642	MCF-7	breast:	n/a	n/a
20	STAT3	chr5:9269155-9269260	MCF10A-Er-Src	breast:	n/a	n/a
21	FOS	chr5:9269128-9269541	MCF10A-Er-Src	breast:	n/a	n/a
22	STAT3	chr5:9269237-9269597	MCF10A-Er-Src	breast:	n/a	n/a
23	PBX3	chr5:9269057-9269650	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
SEMA5A	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1012963	0.80[GIH][hapmap]
rs1034743	1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12515412	0.95[EUR][1000 genomes]
rs13174696	0.94[EUR][1000 genomes]
rs1479654	1.00[CEU][hapmap];0.91[JPT][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs1479655	0.95[EUR][1000 genomes]
rs17255732	0.95[EUR][1000 genomes]
rs17255767	0.97[EUR][1000 genomes]
rs1805916	0.83[GIH][hapmap]
rs1805917	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1805918	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1805919	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1805947	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs1805949	1.00[CEU][hapmap];0.91[JPT][hapmap];0.95[EUR][1000 genomes]
rs1805950	1.00[CEU][hapmap];0.91[JPT][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs1805951	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs1805953	0.91[EUR][1000 genomes]
rs2387814	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3777296	0.96[CEU][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes]
rs3777303	1.00[CEU][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3797975	1.00[CEU][hapmap];0.87[JPT][hapmap];0.95[EUR][1000 genomes]
rs3822782	0.96[CEU][hapmap];0.83[JPT][hapmap];0.93[TSI][hapmap]
rs3822786	0.98[EUR][1000 genomes]
rs3912190	1.00[CEU][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes]
rs4320230	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4702617	0.96[CEU][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs4702618	0.97[EUR][1000 genomes]
rs62341975	0.92[EUR][1000 genomes]
rs7717292	1.00[CEU][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes]
rs7717454	0.93[EUR][1000 genomes]
rs7719392	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7726397	0.98[EUR][1000 genomes]
rs7733680	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7734564	0.96[CEU][hapmap];0.91[JPT][hapmap];0.97[EUR][1000 genomes]
rs929305	0.95[CEU][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes]
rs929306	1.00[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1016937	chr5:8824417-9402871	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv537638	chr5:8824417-9402871	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv918004	chr5:8824417-9402871	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
6	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
7	nsv830200	chr5:9081023-9269495	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv597070	chr5:9100211-9280338	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1020815	chr5:9135207-9425649	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv498044	chr5:9143754-9402870	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv530183	chr5:9146506-9413373	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv597071	chr5:9182376-9760599	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1032672	chr5:9182409-9843893	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv1035075	chr5:9182584-9843723	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
15	nsv537641	chr5:9182584-9843723	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
16	nsv1034637	chr5:9182784-9741743	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
17	nsv537642	chr5:9182784-9741743	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
18	nsv1028656	chr5:9196001-9837040	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
19	nsv1016885	chr5:9218932-9575594	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
20	nsv1026078	chr5:9222811-9591290	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
21	nsv1022137	chr5:9225121-9745434	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
22	nsv537643	chr5:9225121-9745434	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
23	nsv4708	chr5:9245266-9290172	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9250000-9274200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr5:9265800-9289000	Weak transcription	Aorta	Aorta
3	chr5:9266000-9272200	Weak transcription	Pancreas	Pancrea
4	chr5:9266200-9271200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:9266200-9271800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:9266200-9272000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:9266400-9270400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr5:9266400-9270400	Enhancers	HMEC	breast
9	chr5:9266400-9271800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:9266400-9271800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr5:9266400-9273600	Weak transcription	Fetal Stomach	stomach
12	chr5:9266400-9284800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:9266600-9271600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:9266600-9278600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:9267000-9275600	Weak transcription	NHLF	lung
16	chr5:9267200-9278600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr5:9267200-9285200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr5:9267600-9271600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:9267800-9270200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:9268200-9269800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:9268200-9271200	Weak transcription	Esophagus	oesophagus
22	chr5:9268400-9269600	Enhancers	NH-A	brain
23	chr5:9268800-9281400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr5:9269000-9269600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr5:9269200-9269400	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr5:9269200-9269600	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr5:9269200-9269600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:9269200-9269600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr5:9269200-9270400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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