Variant report

Variant	rs2525098
Chromosome Location	chr17:46077360-46077361
allele	G/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	CTCF	chr17:46077043-46077363	K562	blood:	n/a	chr17:46077206-46077214
2	CTCF	chr17:46077220-46077370	HEK293	kidney:	n/a	n/a
3	CTCF	chr17:46077042-46077440	K562	blood:	n/a	chr17:46077206-46077214
4	CTCF	chr17:46077220-46077370	Caco-2	colon:	n/a	n/a
5	CEBPB	chr17:46077033-46077366	IMR90	lung:	n/a	n/a
6	CEBPB	chr17:46077020-46077375	HepG2	liver:	n/a	n/a
7	CEBPB	chr17:46077015-46077451	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46047115..46050048-chr17:46075533..46077931,3	MCF-7	breast:
2	chr17:46072351..46074224-chr17:46077019..46079438,2	MCF-7	breast:
3	chr17:46075615..46077528-chr17:46123330..46125868,2	MCF-7	breast:
4	chr17:46064874..46067902-chr17:46077258..46079817,3	K562	blood:
5	chr17:46066387..46068128-chr17:46076064..46078648,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264701	TF binding region
ENSG00000264701	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000108465	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11079804	0.88[CHB][hapmap]
rs11545723	0.94[CHB][hapmap]
rs1476578	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1476579	0.88[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs17617250	0.87[CHB][hapmap]
rs2003477	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2003478	0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2255697	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2255815	0.96[ASN][1000 genomes]
rs2525084	0.95[ASN][1000 genomes]
rs2525085	0.97[ASN][1000 genomes]
rs2525087	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs2525088	0.88[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2525090	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2525091	0.97[ASN][1000 genomes]
rs2525092	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2525093	1.00[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs2525094	0.80[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2525096	0.88[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2597161	0.97[ASN][1000 genomes]
rs2597165	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2597168	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2597171	0.94[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs2597172	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.82[MKK][hapmap];0.97[ASN][1000 genomes]
rs2597173	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2597174	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2597179	1.00[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs2597180	0.96[ASN][1000 genomes]
rs2597181	0.96[ASN][1000 genomes]
rs2875746	0.88[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.82[LWK][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2905845	0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2905846	0.97[ASN][1000 genomes]
rs2905848	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2905849	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2905850	0.99[ASN][1000 genomes]
rs2905851	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2905852	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2905853	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs34190379	0.91[ASN][1000 genomes]
rs35653190	0.86[ASN][1000 genomes]
rs4793734	0.94[CHB][hapmap]
rs4794225	0.82[CHB][hapmap]
rs62064873	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6503949	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs729785	1.00[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs729786	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs737130	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs739853	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7406338	0.93[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7503584	1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs8076314	0.97[ASN][1000 genomes]
rs885634	0.99[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	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2525098	ASB16	cis	parietal	SCAN
rs2525098	ATP6V0A1	cis	parietal	SCAN
rs2525098	ATP5G1	cis	cerebellum	SCAN
rs2525098	NFE2L1	cis	parietal	SCAN
rs2525098	PNPO	cis	cerebellum	SCAN
rs2525098	PNPO	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46061800-46079600	Weak transcription	Right Atrium	heart
2	chr17:46068000-46079800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr17:46069000-46079600	Weak transcription	Fetal Thymus	thymus
4	chr17:46073200-46078800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr17:46073400-46081000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr17:46073800-46078800	Weak transcription	Brain Germinal Matrix	brain
7	chr17:46073800-46079600	Weak transcription	Esophagus	oesophagus
8	chr17:46074200-46078800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr17:46074200-46079600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr17:46074200-46079600	Weak transcription	K562	blood
11	chr17:46074200-46079800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr17:46075600-46079000	Weak transcription	Adipose Nuclei	Adipose
13	chr17:46076400-46077400	Enhancers	HSMM	muscle
14	chr17:46076400-46077600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr17:46076400-46079400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr17:46076400-46084600	Enhancers	Fetal Brain Male	brain
17	chr17:46076600-46077800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr17:46076600-46077800	Enhancers	Muscle Satellite Cultured Cells	--
19	chr17:46076800-46077400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr17:46076800-46077600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr17:46076800-46077800	Enhancers	Osteobl	bone
22	chr17:46076800-46078000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr17:46076800-46078000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr17:46076800-46085600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr17:46077000-46077400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr17:46077000-46077400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr17:46077000-46077400	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr17:46077000-46077400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr17:46077000-46077400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr17:46077000-46077400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr17:46077000-46077400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr17:46077000-46077400	Enhancers	Brain Anterior Caudate	brain
33	chr17:46077000-46077400	Enhancers	HSMMtube	muscle
34	chr17:46077000-46077400	Enhancers	NH-A	brain
35	chr17:46077000-46077600	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr17:46077000-46077600	Enhancers	H1 Cell Line	embryonic stem cell
37	chr17:46077000-46077600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr17:46077000-46077600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr17:46077000-46077600	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr17:46077000-46077600	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr17:46077000-46077600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr17:46077000-46077600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr17:46077000-46077600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr17:46077000-46077600	Enhancers	HUVEC	blood vessel
45	chr17:46077000-46077800	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr17:46077000-46077800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr17:46077000-46078000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr17:46077000-46078000	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr17:46077000-46078000	Enhancers	Fetal Brain Female	brain
50	chr17:46077000-46078000	Enhancers	Placenta	Placenta

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