Variant report

Variant	rs2597171
Chromosome Location	chr17:46052162-46052163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45916805..45918645-chr17:46049307..46052220,2	MCF-7	breast:
2	chr17:46046297..46048098-chr17:46050701..46053030,2	MCF-7	breast:
3	chr17:46048432..46050374-chr17:46050535..46053358,3	MCF-7	breast:
4	chr17:46048621..46053225-chr17:46056317..46060413,5	K562	blood:

Variant related genes	Relation type
ENSG00000108465	Chromatin interaction
ENSG00000141295	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs11079804	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs11545723	0.89[CHB][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap]
rs1476578	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1476579	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17617250	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs2003477	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003478	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2255697	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255815	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2525084	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525085	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525087	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525088	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525090	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525091	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525092	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525093	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525094	0.92[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525096	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2525098	0.94[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs2525103	0.85[TSI][hapmap]
rs2597161	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597165	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2597168	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597172	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597173	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597174	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]
rs2597179	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597180	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2597181	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2875746	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2905845	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905846	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2905848	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905849	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905850	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905851	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905852	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905853	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34190379	0.94[ASN][1000 genomes]
rs35653190	0.83[ASN][1000 genomes]
rs4793734	0.89[CHB][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap]
rs62064873	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6503949	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729785	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729786	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737130	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs739853	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7406338	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7503584	0.84[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.94[ASN][1000 genomes]
rs8076314	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885634	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2597171	PNPO	cis	parietal	SCAN
rs2597171	C17orf57	cis	parietal	SCAN
rs2597171	ETV4	cis	parietal	SCAN
rs2597171	ATP6V0A1	cis	parietal	SCAN
rs2597171	PNPO	cis	cerebellum	SCAN
rs2597171	NFE2L1	cis	parietal	SCAN
rs2597171	ASB16	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46049000-46052200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:46049000-46055200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr17:46049000-46056000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr17:46049400-46052800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:46049600-46052800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr17:46049600-46056200	Weak transcription	Psoas Muscle	Psoas
7	chr17:46049600-46059600	Weak transcription	Fetal Heart	heart
8	chr17:46049800-46052200	Weak transcription	NH-A	brain
9	chr17:46049800-46058200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr17:46049800-46066600	Weak transcription	Small Intestine	intestine
11	chr17:46050000-46053000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr17:46050000-46054800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr17:46050000-46055800	Weak transcription	Fetal Brain Male	brain
14	chr17:46050000-46056200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr17:46050200-46054800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr17:46050200-46056000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr17:46050200-46056000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr17:46050200-46060400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr17:46050200-46060400	Strong transcription	Osteobl	bone
20	chr17:46050200-46061800	Strong transcription	NHLF	lung
21	chr17:46050200-46062000	Strong transcription	NHEK	skin
22	chr17:46050200-46062200	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr17:46050200-46062800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr17:46050200-46063000	Strong transcription	Fetal Muscle Trunk	muscle
25	chr17:46050200-46063400	Strong transcription	Fetal Stomach	stomach
26	chr17:46050400-46053600	Strong transcription	K562	blood
27	chr17:46050400-46056800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr17:46050400-46058000	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr17:46050400-46060800	Strong transcription	Ovary	ovary
30	chr17:46050400-46061000	Strong transcription	A549	lung
31	chr17:46050400-46061200	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr17:46050400-46061400	Strong transcription	HepG2	liver
33	chr17:46050400-46062000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr17:46050400-46062200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr17:46050400-46063000	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr17:46050600-46056000	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr17:46050600-46056000	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr17:46050600-46056200	Strong transcription	Duodenum Mucosa	Duodenum
39	chr17:46050600-46057000	Strong transcription	Dnd41	blood
40	chr17:46050600-46058000	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr17:46050600-46061800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr17:46050600-46062200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr17:46050600-46062200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr17:46050800-46053400	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr17:46050800-46053600	Strong transcription	HMEC	breast
46	chr17:46050800-46053800	Strong transcription	Pancreas	Pancrea
47	chr17:46050800-46055400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr17:46050800-46056000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr17:46050800-46056000	Strong transcription	GM12878-XiMat	blood
50	chr17:46050800-46057200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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