Variant report

Variant	rs2597174
Chromosome Location	chr17:46057029-46057030
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	SMC3	chr17:46055523-46058664	SK-N-SH	brain:	n/a	chr17:46058259-46058269 chr17:46055894-46055908 chr17:46057121-46057129
2	POLR2A	chr17:46057018-46057189	K562	blood:	n/a	n/a
3	GATA3	chr17:46056926-46057545	SH-SY5Y	brain:	n/a	n/a
4	RAD21	chr17:46055608-46058810	SK-N-SH	brain:	n/a	chr17:46055897-46055906 chr17:46058189-46058201 chr17:46056305-46056315 chr17:46055895-46055902 chr17:46055893-46055912 chr17:46055898-46055910 chr17:46055894-46055908 chr17:46058259-46058269

No.	Distal block	Cell Line	Cell type
1	chr17:46048621..46053225-chr17:46056317..46060413,5	K562	blood:
2	chr17:46047439..46051573-chr17:46055956..46059590,5	MCF-7	breast:
3	chr17:46047245..46051740-chr17:46053378..46057507,6	MCF-7	breast:
4	chr17:46034267..46036157-chr17:46054956..46057577,2	MCF-7	breast:
5	chr17:46046859..46048450-chr17:46055513..46058232,2	K562	blood:

Variant related genes	Relation type
CDK5RAP3	TF binding region
ENSG00000108465	Chromatin interaction
ENSG00000167183	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs11079804	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs11545723	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs1476578	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1476579	0.88[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17617250	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs2003477	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003478	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2255697	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255815	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2525084	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525085	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525088	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525091	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525092	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525093	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525094	0.80[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525096	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2525098	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]
rs2525103	0.85[TSI][hapmap]
rs2597161	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597165	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2597168	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597171	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597173	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597180	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2597181	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2875746	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2905845	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905846	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2905848	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905849	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905850	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905852	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905853	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34190379	0.94[ASN][1000 genomes]
rs35653190	0.83[ASN][1000 genomes]
rs4793734	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs4794225	0.82[CHB][hapmap]
rs62064873	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6503949	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737130	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs739853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7406338	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7503584	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[MEX][hapmap];0.94[ASN][1000 genomes]
rs8076314	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885634	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	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
3	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2597174	HOXB2	cis	multi-tissue	Pritchard
rs2597174	ETV4	cis	parietal	SCAN
rs2597174	PNPO	cis	cerebellum	SCAN
rs2597174	PNPO	cis	parietal	SCAN
rs2597174	C17orf57	cis	parietal	SCAN
rs2597174	NFE2L1	cis	parietal	SCAN
rs2597174	ASB16	cis	parietal	SCAN
rs2597174	ATP6V0A1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46049600-46059600	Weak transcription	Fetal Heart	heart
2	chr17:46049800-46058200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr17:46049800-46066600	Weak transcription	Small Intestine	intestine
4	chr17:46050200-46060400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr17:46050200-46060400	Strong transcription	Osteobl	bone
6	chr17:46050200-46061800	Strong transcription	NHLF	lung
7	chr17:46050200-46062000	Strong transcription	NHEK	skin
8	chr17:46050200-46062200	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr17:46050200-46062800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr17:46050200-46063000	Strong transcription	Fetal Muscle Trunk	muscle
11	chr17:46050200-46063400	Strong transcription	Fetal Stomach	stomach
12	chr17:46050400-46058000	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr17:46050400-46060800	Strong transcription	Ovary	ovary
14	chr17:46050400-46061000	Strong transcription	A549	lung
15	chr17:46050400-46061200	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr17:46050400-46061400	Strong transcription	HepG2	liver
17	chr17:46050400-46062000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr17:46050400-46062200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr17:46050400-46063000	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr17:46050600-46058000	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr17:46050600-46061800	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr17:46050600-46062200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr17:46050600-46062200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr17:46050800-46057200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr17:46050800-46057800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr17:46050800-46057800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr17:46050800-46058000	Strong transcription	Brain Cingulate Gyrus	brain
28	chr17:46050800-46059000	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr17:46050800-46059200	Strong transcription	Liver	Liver
30	chr17:46050800-46059200	Strong transcription	Spleen	Spleen
31	chr17:46050800-46059600	Strong transcription	Brain Anterior Caudate	brain
32	chr17:46050800-46060000	Strong transcription	Brain Angular Gyrus	brain
33	chr17:46050800-46060200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr17:46050800-46060200	Strong transcription	Adipose Nuclei	Adipose
35	chr17:46050800-46060200	Strong transcription	Gastric	stomach
36	chr17:46050800-46060800	Strong transcription	Lung	lung
37	chr17:46050800-46061000	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr17:46050800-46061200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr17:46050800-46061600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr17:46050800-46061600	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr17:46050800-46061800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr17:46050800-46062000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr17:46050800-46062000	Strong transcription	Primary B cells from peripheral blood	blood
44	chr17:46050800-46062200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr17:46050800-46062400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr17:46050800-46062600	Strong transcription	Fetal Intestine Small	intestine
47	chr17:46050800-46062800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr17:46050800-46063000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr17:46050800-46063000	Strong transcription	Fetal Muscle Leg	muscle
50	chr17:46051000-46057800	Strong transcription	Brain Hippocampus Middle	brain

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