Variant report

Variant	rs62523279
Chromosome Location	chr8:95225308-95225309
allele	A/C
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	NFIC	chr8:95224334-95226506	SK-N-SH	brain:	n/a	chr8:95224736-95224753 chr8:95224736-95224752 chr8:95224726-95224754
2	GATA3	chr8:95224253-95226549	SK-N-SH	brain:	n/a	chr8:95225843-95225855 chr8:95225841-95225857 chr8:95225848-95225855
3	PBX3	chr8:95224511-95225386	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr8:95224358-95225401	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr8:95224343-95226504	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr8:95224375-95226516	SK-N-SH	brain:	n/a	n/a
7	FOSL2	chr8:95224531-95225340	SK-N-SH	brain:	n/a	n/a
8	JUND	chr8:95224464-95225335	SK-N-SH	brain:	n/a	n/a
9	NFIC	chr8:95224354-95225314	SK-N-SH	brain:	n/a	chr8:95224736-95224753 chr8:95224736-95224752 chr8:95224726-95224754
10	EP300	chr8:95224352-95225420	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:95223330..95225554-chr8:95230383..95232655,2	MCF-7	breast:
2	chr8:95224589..95225412-chr8:95369113..95370095,2	MCF-7	breast:

Variant related genes	Relation type
CDH17	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10504934	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10956904	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10956905	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10956906	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11777372	0.97[ASN][1000 genomes]
rs11779791	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11786049	0.82[EUR][1000 genomes]
rs12114629	0.97[ASN][1000 genomes]
rs1350283	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17727794	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1817245	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1971965	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2607058	0.80[ASN][1000 genomes]
rs2613221	0.81[ASN][1000 genomes]
rs2613225	0.83[ASN][1000 genomes]
rs2623155	0.83[ASN][1000 genomes]
rs2623156	0.83[ASN][1000 genomes]
rs2623157	0.83[ASN][1000 genomes]
rs34689002	0.82[ASN][1000 genomes]
rs3757995	0.81[ASN][1000 genomes]
rs4587298	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4734271	0.80[EUR][1000 genomes]
rs55795711	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56129387	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59773910	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60945589	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62523262	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62523265	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62523266	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62523277	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62523278	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6981215	0.99[ASN][1000 genomes]
rs723360	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs755917	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7819765	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs874019	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9642922	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9643341	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs978639	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024907	chr8:95188944-95296378	Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv539677	chr8:95188944-95296378	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1022972	chr8:95189085-95245392	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1024893	chr8:95189085-95293557	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv518636	chr8:95196794-95233336	Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv539678	chr8:95197036-95225644	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1030292	chr8:95198982-95231692	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv522024	chr8:95199215-95232449	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1020665	chr8:95199302-95232062	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1022489	chr8:95212660-95273564	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv539679	chr8:95212660-95273564	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv1035036	chr8:95213244-95283014	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv831401	chr8:95218297-95393968	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95220800-95230800	Weak transcription	Small Intestine	intestine
2	chr8:95222000-95229600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr8:95222000-95230000	Weak transcription	Fetal Intestine Large	intestine
4	chr8:95223600-95231000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr8:95224200-95226400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr8:95224200-95226400	Enhancers	A549	lung
7	chr8:95224400-95225400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr8:95224400-95225400	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr8:95224400-95225400	Enhancers	Osteobl	bone
10	chr8:95224400-95226400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr8:95224400-95226400	Enhancers	Hela-S3	cervix
12	chr8:95224400-95226600	Enhancers	NH-A	brain
13	chr8:95224400-95228200	Weak transcription	Fetal Intestine Small	intestine
14	chr8:95224600-95225600	Enhancers	Dnd41	blood
15	chr8:95225000-95225400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr8:95225000-95225400	Enhancers	HMEC	breast
17	chr8:95225000-95225800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr8:95225200-95225400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr8:95225200-95225400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr8:95225200-95229400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr8:95225200-95229600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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