Variant report

Variant	rs17725163
Chromosome Location	chr4:56475447-56475448
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:56465744..56469712-chr4:56475129..56477433,3	K562	blood:
2	chr4:56466882..56469712-chr4:56475375..56477433,2	K562	blood:
3	chr4:56472523..56475869-chr4:56480434..56484043,4	K562	blood:
4	chr4:56474369..56476951-chr4:56481028..56484786,4	K562	blood:
5	chr4:56472621..56475219-chr4:56475225..56477153,2	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10000512	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10011089	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10011801	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10012559	1.00[CHB][hapmap]
rs10017749	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10018932	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10026315	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10026676	0.96[ASN][1000 genomes]
rs10029142	1.00[ASN][1000 genomes]
rs1021306	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs1021307	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs10462028	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs11240	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11732481	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs11732723	0.86[JPT][hapmap]
rs11932595	1.00[CHB][hapmap]
rs11943456	0.86[JPT][hapmap]
rs13434995	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17721497	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs17722979	1.00[CHB][hapmap];0.91[CHD][hapmap]
rs17725110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17776975	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs17781708	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1801260	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs1873090	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1873091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1979604	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs1979605	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2070062	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2130040	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2412664	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs2412665	0.98[ASN][1000 genomes]
rs2412666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28416150	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28435401	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28451532	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28473211	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28564902	1.00[ASN][1000 genomes]
rs28708716	0.95[ASN][1000 genomes]
rs28713371	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28756087	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3792603	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap]
rs3805383	0.96[ASN][1000 genomes]
rs3805385	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805387	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805388	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805389	1.00[ASN][1000 genomes]
rs41324951	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs4336288	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs4865012	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs550144	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs55849318	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55893990	0.83[AMR][1000 genomes]
rs56288855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57178140	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59571323	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62308665	1.00[ASN][1000 genomes]
rs62308667	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62308708	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62310884	0.81[ASN][1000 genomes]
rs6554290	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap]
rs6554291	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap]
rs6802	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6830728	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6842960	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6851971	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6853506	1.00[CHB][hapmap]
rs6858749	0.86[JPT][hapmap]
rs73236165	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73236170	0.86[AMR][1000 genomes]
rs7659095	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7660668	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7665846	0.91[JPT][hapmap]
rs7698022	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs880358	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs972446	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs9790448	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9993599	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs9996936	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv998179	chr4:56425126-56694339	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv932636	chr4:56438618-56667329	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17725163	TMEM165	cis	parietal	SCAN
rs17725163	SRD5A2L	cis	multi-tissue	Pritchard
rs17725163	TMEM165	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56464200-56475800	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr4:56465400-56479400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:56465600-56476000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr4:56469800-56481200	Weak transcription	Esophagus	oesophagus
5	chr4:56470400-56478800	Strong transcription	K562	blood
6	chr4:56472400-56476600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:56473600-56491600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr4:56474000-56475800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr4:56474600-56477200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:56474800-56475800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:56474800-56476200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr4:56474800-56476200	Enhancers	NHDF-Ad	bronchial
13	chr4:56474800-56476400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr4:56474800-56476400	Enhancers	HSMM	muscle
15	chr4:56475200-56475600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:56475200-56475600	Flanking Active TSS	HMEC	breast
17	chr4:56475200-56475600	Flanking Active TSS	NHEK	skin
18	chr4:56475200-56476000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr4:56475200-56476200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:56475200-56476400	Enhancers	Stomach Mucosa	stomach
21	chr4:56475400-56475600	Flanking Active TSS	Thymus	Thymus
22	chr4:56475400-56475800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:56475400-56476200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:56475400-56476200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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