Variant report

Variant	rs2086650
Chromosome Location	chr1:10640438-10640439
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10622081..10624385-chr1:10637309..10640742,3	K562	blood:
2	chr1:10632331..10635200-chr1:10638262..10640541,2	K562	blood:
3	chr1:10638213..10640630-chr1:10641912..10644179,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10157111	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10157119	0.85[ASN][1000 genomes]
rs10746495	0.84[ASN][1000 genomes]
rs10779739	0.85[ASN][1000 genomes]
rs10779743	0.85[ASN][1000 genomes]
rs10779744	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10864463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11121584	0.84[ASN][1000 genomes]
rs11121588	0.85[ASN][1000 genomes]
rs11121589	0.85[ASN][1000 genomes]
rs11121593	0.86[ASN][1000 genomes]
rs11121594	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12033275	0.90[JPT][hapmap]
rs12128630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12133103	0.84[ASN][1000 genomes]
rs12565494	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12753364	0.86[ASN][1000 genomes]
rs17035189	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2039176	0.83[ASN][1000 genomes]
rs2480771	0.85[ASN][1000 genomes]
rs2480772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2480773	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2480775	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2480780	0.91[JPT][hapmap]
rs2480781	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2506878	0.85[JPT][hapmap]
rs2506897	0.83[ASN][1000 genomes]
rs2506898	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2506900	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2988398	0.84[ASN][1000 genomes]
rs34230252	0.86[ASN][1000 genomes]
rs35409029	0.85[ASN][1000 genomes]
rs35612158	0.85[ASN][1000 genomes]
rs4240914	0.91[JPT][hapmap]
rs4240915	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4617401	0.84[ASN][1000 genomes]
rs4845936	0.86[ASN][1000 genomes]
rs4846230	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4846231	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4846232	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4846233	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4846237	0.84[ASN][1000 genomes]
rs61777207	0.85[ASN][1000 genomes]
rs61777208	0.85[ASN][1000 genomes]
rs6540937	0.86[ASN][1000 genomes]
rs6540938	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6658073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6661757	0.85[ASN][1000 genomes]
rs6663688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6663898	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6664134	0.86[ASN][1000 genomes]
rs6676491	0.95[AFR][1000 genomes]
rs6687502	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6687622	0.86[ASN][1000 genomes]
rs6700023	0.83[ASN][1000 genomes]
rs6700886	0.81[ASN][1000 genomes]
rs710130	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs747124	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512467	0.90[JPT][hapmap]
rs7519424	0.85[ASN][1000 genomes]
rs7534954	0.82[ASN][1000 genomes]
rs7548453	0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs944191	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9660006	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9660218	0.89[YRI][hapmap];0.90[AFR][1000 genomes]
rs9661121	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
4	nsv1009596	chr1:10626249-10652605	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv517464	chr1:10638604-10643197	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv818777	chr1:10638604-10643197	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2086650	PEX14	cis	multi-tissue	Pritchard
rs2086650	Hs.211939	cis	multi-tissue	Pritchard
rs2086650	PGD	cis	Muscle Skeletal	GTEx
rs2086650	PEX14	cis	Lymphoblastoid	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10589400-10664800	Weak transcription	Aorta	Aorta
2	chr1:10603000-10659000	Weak transcription	Primary B cells from cord blood	blood
3	chr1:10605000-10659000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr1:10607600-10641400	Weak transcription	Lung	lung
5	chr1:10623600-10645600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:10624800-10646000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:10627800-10641000	Weak transcription	Fetal Stomach	stomach
8	chr1:10627800-10643000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:10628000-10650200	Weak transcription	Fetal Lung	lung
10	chr1:10628400-10661600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr1:10628800-10651200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:10629800-10643600	Weak transcription	Fetal Muscle Leg	muscle
13	chr1:10629800-10659000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:10631800-10659200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:10632600-10698000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:10635800-10650800	Weak transcription	HSMMtube	muscle
17	chr1:10636000-10650600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:10636200-10655600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:10636200-10656000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:10636400-10656200	Weak transcription	NHEK	skin
21	chr1:10636600-10658000	Weak transcription	Spleen	Spleen
22	chr1:10637000-10641600	Weak transcription	Adipose Nuclei	Adipose
23	chr1:10637400-10652200	Weak transcription	Fetal Intestine Small	intestine
24	chr1:10637400-10659000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:10638200-10642400	Weak transcription	Primary T cells from cord blood	blood
26	chr1:10638400-10645000	Weak transcription	Liver	Liver
27	chr1:10638400-10657400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:10638400-10661600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:10638600-10651600	Weak transcription	Left Ventricle	heart
30	chr1:10638600-10661600	Weak transcription	Primary B cells from peripheral blood	blood
31	chr1:10638800-10644600	Weak transcription	HepG2	liver
32	chr1:10639000-10641200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:10639000-10643800	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr1:10639000-10651200	Weak transcription	HSMM	muscle
35	chr1:10639000-10652800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr1:10639200-10643200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:10639200-10650600	Weak transcription	A549	lung
38	chr1:10639800-10659200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr1:10640000-10641000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:10640000-10641200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:10640400-10656600	Weak transcription	Placenta	Placenta

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