Variant report

Variant	rs9660006
Chromosome Location	chr1:10617272-10617273
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10574766..10576583-chr1:10614783..10617657,2	MCF-7	breast:
2	chr1:10615907..10618063-chr1:10619537..10622754,3	K562	blood:
3	chr1:10610347..10612190-chr1:10616959..10619144,2	K562	blood:

Extended variants
information (count: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10157111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10157119	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746495	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10779739	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10779743	0.97[ASN][1000 genomes]
rs10779744	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10864461	0.86[EUR][1000 genomes]
rs10864463	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];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10864465	0.85[EUR][1000 genomes]
rs11121584	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11121585	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11121588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11121589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11121593	0.98[ASN][1000 genomes]
rs11121594	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11121596	0.86[EUR][1000 genomes]
rs11121597	0.86[EUR][1000 genomes]
rs12033275	1.00[CEU][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs12128630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129678	0.86[EUR][1000 genomes]
rs12133103	0.96[ASN][1000 genomes]
rs12565494	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12750901	0.92[ASN][1000 genomes]
rs12753364	0.98[ASN][1000 genomes]
rs17035156	0.88[GIH][hapmap]
rs2039175	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2039176	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2086650	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2183377	0.89[EUR][1000 genomes]
rs2480771	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2480772	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2480773	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2480775	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2480780	0.84[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs2480781	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2480786	0.84[GIH][hapmap]
rs2480787	0.85[EUR][1000 genomes]
rs2480789	0.93[GIH][hapmap]
rs2483678	0.88[GIH][hapmap]
rs2506878	0.93[GIH][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2506887	0.88[GIH][hapmap]
rs2506888	0.82[EUR][1000 genomes]
rs2506897	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2506898	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2506900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2988398	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34230252	0.98[ASN][1000 genomes]
rs35409029	1.00[ASN][1000 genomes]
rs35612158	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4240914	0.84[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs4240915	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4617401	0.89[ASN][1000 genomes]
rs4845936	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4846230	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4846237	0.96[ASN][1000 genomes]
rs58788814	0.86[EUR][1000 genomes]
rs61777207	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61777208	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540937	0.98[ASN][1000 genomes]
rs6540938	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[ASN][1000 genomes]
rs6658073	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661757	0.98[ASN][1000 genomes]
rs6663688	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6663898	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6664134	0.98[ASN][1000 genomes]
rs6681221	0.86[EUR][1000 genomes]
rs6687502	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs6687622	0.98[ASN][1000 genomes]
rs6700023	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6700886	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs710130	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs72641424	0.85[EUR][1000 genomes]
rs72641427	0.82[EUR][1000 genomes]
rs747124	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7512467	1.00[CEU][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs7519424	1.00[ASN][1000 genomes]
rs7524790	0.92[ASN][1000 genomes]
rs7534954	0.95[ASN][1000 genomes]
rs7545184	0.88[EUR][1000 genomes]
rs944191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9661121	0.99[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	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1015079	chr1:10611403-10645176	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9660006	PEX14	cis	Lymphoblastoid	GTEx
rs9660006	VAMP3	cis	parietal	SCAN
rs9660006	PEX14	cis	multi-tissue	Pritchard
rs9660006	Hs.211939	cis	multi-tissue	Pritchard

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10589400-10664800	Weak transcription	Aorta	Aorta
2	chr1:10591000-10639400	Weak transcription	Hela-S3	cervix
3	chr1:10591400-10629200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:10598600-10621800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:10600000-10619600	Weak transcription	Brain Substantia Nigra	brain
6	chr1:10601200-10619600	Weak transcription	Brain Anterior Caudate	brain
7	chr1:10602000-10619400	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:10602000-10639600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:10602600-10619400	Weak transcription	NHEK	skin
10	chr1:10602600-10624000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:10603000-10659000	Weak transcription	Primary B cells from cord blood	blood
12	chr1:10604600-10619600	Weak transcription	Thymus	Thymus
13	chr1:10604600-10621400	Weak transcription	Dnd41	blood
14	chr1:10604600-10623800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr1:10604800-10621200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:10605000-10659000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr1:10605400-10621200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:10606000-10638000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr1:10607200-10619600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:10607600-10623200	Weak transcription	Fetal Stomach	stomach
21	chr1:10607600-10636800	Weak transcription	Primary T cells from cord blood	blood
22	chr1:10607600-10636800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:10607600-10641400	Weak transcription	Lung	lung
24	chr1:10609800-10624200	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr1:10610600-10619600	Weak transcription	Gastric	stomach
26	chr1:10611200-10619600	Weak transcription	Fetal Intestine Small	intestine
27	chr1:10611800-10624000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr1:10613600-10622000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:10613800-10621000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:10614000-10619600	Weak transcription	Pancreas	Pancrea
31	chr1:10614000-10621000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:10614000-10623400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:10615400-10617800	Enhancers	K562	blood
34	chr1:10616200-10620600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:10616200-10621200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:10616400-10617800	Enhancers	HepG2	liver
37	chr1:10616400-10619400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr1:10616400-10619600	Weak transcription	Psoas Muscle	Psoas
39	chr1:10616400-10621200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:10616400-10621200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:10616400-10621200	Weak transcription	HMEC	breast
42	chr1:10616400-10621400	Weak transcription	Spleen	Spleen
43	chr1:10616400-10623200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:10616400-10623400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:10616400-10633600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:10616400-10638200	Weak transcription	Esophagus	oesophagus
47	chr1:10616600-10617800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr1:10616600-10619600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:10616600-10619600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:10616600-10619600	Weak transcription	Right Atrium	heart

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