Variant report

Variant	rs10873246
Chromosome Location	chr14:72153693-72153694
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:72152429..72155391-chr14:72157958..72160807,2	K562	blood:

Extended variants
information (count: 76 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10132111	0.82[AFR][1000 genomes]
rs10133626	1.00[JPT][hapmap]
rs10135680	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10138557	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10139519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1029570	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10483836	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1204995	0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs1204996	1.00[JPT][hapmap]
rs1204997	0.82[AFR][1000 genomes]
rs12433040	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12880188	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.81[ASN][1000 genomes]
rs12880611	0.86[AFR][1000 genomes]
rs12881957	0.86[AFR][1000 genomes]
rs12885344	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12889866	0.86[AFR][1000 genomes]
rs12892512	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12896900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12896986	0.86[AFR][1000 genomes]
rs17767553	0.86[AFR][1000 genomes]
rs17767680	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs17767686	0.81[ASN][1000 genomes]
rs1859643	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1981588	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2108057	0.91[CEU][hapmap]
rs2190240	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2214836	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2286136	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs2332638	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2332640	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2332641	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34169215	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs34320622	0.86[AFR][1000 genomes]
rs34347034	0.86[AFR][1000 genomes]
rs34480562	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35231795	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35415083	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35680546	0.86[AFR][1000 genomes]
rs35760654	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36072220	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3784062	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3784064	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3784066	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3825719	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4140797	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4319698	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4899398	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];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4902938	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4902941	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4902942	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55883127	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61989373	0.86[AFR][1000 genomes]
rs61989374	0.86[AFR][1000 genomes]
rs61989377	0.86[AFR][1000 genomes]
rs61989383	0.81[ASN][1000 genomes]
rs6574015	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6574016	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7140501	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7142343	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7144299	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7144829	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7148679	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7154787	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7154841	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7156313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7157241	0.81[ASN][1000 genomes]
rs8003478	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8006300	0.91[CEU][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs8008605	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8014349	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8017775	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9323561	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9672060	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.81[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	esv3398985	chr14:71927884-72404676	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv530794	chr14:72113818-73034008	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1047559	chr14:72151736-72282151	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10873246	PCNX	cis	parietal	SCAN
rs10873246	COQ6	cis	parietal	SCAN
rs10873246	PCNX	cis	cerebellum	SCAN
rs10873246	SIPA1L1	cis	cerebellum	SCAN
rs10873246	SMOC1	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72088200-72159600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr14:72118600-72191400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr14:72126200-72159800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr14:72128000-72167800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr14:72129400-72196800	Weak transcription	Right Ventricle	heart
6	chr14:72131800-72154000	Weak transcription	Fetal Heart	heart
7	chr14:72134200-72159000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr14:72139600-72153800	Weak transcription	Fetal Lung	lung
9	chr14:72139800-72155200	Weak transcription	Placenta	Placenta
10	chr14:72140000-72156800	Weak transcription	Fetal Thymus	thymus
11	chr14:72140000-72165800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr14:72140600-72176000	Weak transcription	Hela-S3	cervix
13	chr14:72142000-72191400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr14:72142600-72159000	Weak transcription	Brain Germinal Matrix	brain
15	chr14:72142600-72159000	Weak transcription	NH-A	brain
16	chr14:72142600-72159200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr14:72142600-72159600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr14:72142600-72159800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr14:72147800-72185000	Strong transcription	Primary B cells from peripheral blood	blood
20	chr14:72148000-72161600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr14:72148200-72156800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr14:72148200-72170000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr14:72148200-72175800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr14:72148200-72200400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr14:72148600-72165000	Weak transcription	Fetal Brain Male	brain
26	chr14:72149000-72177800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr14:72149000-72186200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr14:72149400-72161400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr14:72149800-72153800	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr14:72149800-72176000	Weak transcription	Small Intestine	intestine
31	chr14:72150400-72162600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr14:72150600-72153800	Strong transcription	Brain Anterior Caudate	brain
33	chr14:72150600-72154600	Strong transcription	Dnd41	blood
34	chr14:72150600-72156200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr14:72150800-72154800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr14:72150800-72156200	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr14:72151400-72157400	Weak transcription	Brain Angular Gyrus	brain
38	chr14:72151400-72169600	Weak transcription	Fetal Brain Female	brain
39	chr14:72151600-72154200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr14:72151600-72154400	Weak transcription	Ovary	ovary
41	chr14:72151600-72171800	Weak transcription	Left Ventricle	heart
42	chr14:72151600-72188000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr14:72151800-72156800	Weak transcription	Pancreas	Pancrea
44	chr14:72151800-72171600	Weak transcription	Colonic Mucosa	Colon
45	chr14:72152000-72153800	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr14:72152200-72165600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr14:72152400-72155200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr14:72152400-72159200	Weak transcription	Lung	lung
49	chr14:72152400-72159400	Weak transcription	Aorta	Aorta
50	chr14:72152400-72159600	Weak transcription	Primary T cells fromperipheralblood	blood

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