Variant report

Variant	rs17011666
Chromosome Location	chr1:222798965-222798966
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:222792534..222794480-chr1:222797586..222800158,2	MCF-7	breast:
2	chr1:222798717..222801215-chr1:222815665..222817228,2	K562	blood:
3	chr1:222798057..222800668-chr1:222815376..222816886,2	MCF-7	breast:
4	chr1:222797326..222799070-chr1:222805165..222807968,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10495198	0.86[ASN][1000 genomes]
rs1133220	0.89[ASN][1000 genomes]
rs11485123	0.95[MEX][hapmap]
rs12043288	0.82[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs12138316	0.89[ASN][1000 genomes]
rs1391557	0.83[AMR][1000 genomes]
rs1391558	0.95[MEX][hapmap]
rs1498382	0.83[AMR][1000 genomes]
rs17011681	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17163301	0.82[ASN][1000 genomes]
rs17163313	0.96[ASN][1000 genomes]
rs17163345	0.93[ASN][1000 genomes]
rs17163358	0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17163360	0.92[ASN][1000 genomes]
rs17163363	0.92[ASN][1000 genomes]
rs17465637	0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs17465940	0.83[ASN][1000 genomes]
rs17465982	0.84[ASN][1000 genomes]
rs17532708	0.82[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1909195	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1909197	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2030076	0.85[MEX][hapmap]
rs2088514	0.92[ASW][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.81[AMR][1000 genomes]
rs2133187	0.92[ASN][1000 genomes]
rs2133188	0.86[ASW][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.83[AMR][1000 genomes]
rs2133189	0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2270707	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291832	0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2291834	0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2378584	0.82[ASN][1000 genomes]
rs28709375	0.85[ASN][1000 genomes]
rs2936020	0.81[AMR][1000 genomes]
rs2936023	0.81[AMR][1000 genomes]
rs2936049	0.95[MEX][hapmap]
rs2936051	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2936052	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2936054	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3002146	0.83[AMR][1000 genomes]
rs3002148	0.83[AMR][1000 genomes]
rs3008614	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3008615	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3008616	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3008618	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3008622	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3008625	0.83[AMR][1000 genomes]
rs34032254	0.86[ASN][1000 genomes]
rs34767248	0.82[ASN][1000 genomes]
rs35158675	0.91[ASN][1000 genomes]
rs35175385	0.86[ASN][1000 genomes]
rs35507977	0.90[MEX][hapmap]
rs35626308	0.90[ASN][1000 genomes]
rs35700460	0.92[ASN][1000 genomes]
rs35725247	0.85[ASN][1000 genomes]
rs35806535	0.96[TSI][hapmap]
rs3748626	0.94[ASN][1000 genomes]
rs3811465	0.95[MEX][hapmap]
rs4282830	0.83[ASN][1000 genomes]
rs4575092	0.89[ASN][1000 genomes]
rs4846384	0.95[ASN][1000 genomes]
rs4846770	0.82[ASN][1000 genomes]
rs61824331	0.85[ASN][1000 genomes]
rs61827168	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6683071	0.96[TSI][hapmap]
rs67180937	0.92[ASN][1000 genomes]
rs71524942	0.84[ASN][1000 genomes]
rs9441835	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9441926	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17011666	C1orf58	cis	parietal	SCAN
rs17011666	TAF1A	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222792400-222816600	Weak transcription	Small Intestine	intestine
2	chr1:222792600-222800000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:222792600-222801400	Weak transcription	Lung	lung
4	chr1:222792600-222802200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:222792600-222802200	Weak transcription	Aorta	Aorta
6	chr1:222792600-222816600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:222792600-222817000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:222792800-222802000	Weak transcription	Colonic Mucosa	Colon
9	chr1:222793000-222799000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:222793000-222799800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:222793000-222800200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:222793000-222802200	Weak transcription	HSMMtube	muscle
13	chr1:222793200-222799400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:222793200-222799400	Weak transcription	Thymus	Thymus
15	chr1:222793200-222800000	Weak transcription	Pancreas	Pancrea
16	chr1:222793200-222800000	Weak transcription	Spleen	Spleen
17	chr1:222793200-222800000	Weak transcription	HMEC	breast
18	chr1:222793200-222800000	Weak transcription	NHLF	lung
19	chr1:222793200-222800200	Weak transcription	NHEK	skin
20	chr1:222793200-222800400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:222793200-222801000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:222793200-222801400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:222793200-222802200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:222793200-222802200	Weak transcription	Fetal Intestine Small	intestine
25	chr1:222793200-222802200	Weak transcription	Right Ventricle	heart
26	chr1:222793200-222802800	Weak transcription	Gastric	stomach
27	chr1:222793200-222816600	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr1:222793200-222816600	Weak transcription	Hela-S3	cervix
29	chr1:222793400-222800000	Weak transcription	Brain Substantia Nigra	brain
30	chr1:222793600-222816600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:222794000-222800600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr1:222794000-222806800	Strong transcription	Primary T cells from cord blood	blood
33	chr1:222794200-222802600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:222794200-222805000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:222794400-222800000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:222794600-222800000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:222794600-222800000	Strong transcription	Liver	Liver
38	chr1:222794600-222801400	Weak transcription	GM12878-XiMat	blood
39	chr1:222794600-222803600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:222794600-222807200	Strong transcription	Fetal Thymus	thymus
41	chr1:222794600-222809800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:222794600-222810400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:222794600-222810400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:222794600-222813400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:222794600-222813600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:222794600-222814000	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr1:222794600-222815000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:222794800-222799200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:222794800-222799400	Strong transcription	NHDF-Ad	bronchial
50	chr1:222794800-222799800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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