Variant report

Variant	rs1204997
Chromosome Location	chr14:72183309-72183310
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	chr14:72162902..72165000-chr14:72180965..72183500,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1005605	0.91[ASN][1000 genomes]
rs10132111	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10133626	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10137642	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10139519	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10873246	0.82[AFR][1000 genomes]
rs1204988	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1204992	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1204995	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[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];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1204996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12880188	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs1468373	0.91[ASN][1000 genomes]
rs1981588	0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs2286135	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2286136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3784064	0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs3825719	0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs4140797	0.82[AFR][1000 genomes]
rs4140799	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4899398	0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs7140501	1.00[JPT][hapmap]
rs7142343	0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7148679	0.82[AFR][1000 genomes]
rs7156313	1.00[JPT][hapmap]
rs7350725	0.92[CEU][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs757744	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8006300	0.82[CHD][hapmap]
rs8015004	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9672060	0.93[CHD][hapmap];1.00[JPT][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1204997	PCNX	cis	cerebellum	SCAN
rs1204997	ACOT2	cis	parietal	SCAN
rs1204997	PCNX	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72118600-72191400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr14:72129400-72196800	Weak transcription	Right Ventricle	heart
3	chr14:72142000-72191400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr14:72147800-72185000	Strong transcription	Primary B cells from peripheral blood	blood
5	chr14:72148200-72200400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr14:72149000-72186200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr14:72151600-72188000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr14:72160200-72191400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr14:72160200-72202000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr14:72165200-72202000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr14:72166800-72196400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr14:72167400-72191000	Weak transcription	Fetal Thymus	thymus
13	chr14:72168000-72191800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr14:72168800-72185000	Strong transcription	Primary B cells from cord blood	blood
15	chr14:72168800-72201600	Weak transcription	Stomach Mucosa	stomach
16	chr14:72169200-72191400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr14:72170600-72192200	Weak transcription	Fetal Brain Male	brain
18	chr14:72172000-72196800	Weak transcription	Colonic Mucosa	Colon
19	chr14:72172200-72187200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr14:72172600-72187600	Weak transcription	Fetal Kidney	kidney
21	chr14:72172600-72188000	Weak transcription	Gastric	stomach
22	chr14:72172600-72189200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr14:72172600-72191400	Weak transcription	Fetal Brain Female	brain
24	chr14:72172800-72183400	Weak transcription	Aorta	Aorta
25	chr14:72172800-72188000	Weak transcription	Spleen	Spleen
26	chr14:72176400-72188400	Weak transcription	Lung	lung
27	chr14:72176400-72190400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr14:72176400-72191600	Weak transcription	Pancreas	Pancrea
29	chr14:72176400-72194200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr14:72176400-72197000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr14:72176400-72200000	Weak transcription	Small Intestine	intestine
32	chr14:72176600-72188000	Weak transcription	Esophagus	oesophagus
33	chr14:72176600-72189800	Weak transcription	HepG2	liver
34	chr14:72176600-72191600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr14:72176800-72183600	Enhancers	NHDF-Ad	bronchial
36	chr14:72176800-72188800	Weak transcription	Fetal Intestine Large	intestine
37	chr14:72177000-72183400	Weak transcription	Fetal Stomach	stomach
38	chr14:72177000-72188000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr14:72177200-72186400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr14:72177200-72188000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr14:72177200-72190200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr14:72177200-72191400	Weak transcription	Left Ventricle	heart
43	chr14:72177200-72191400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr14:72177200-72196800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr14:72177400-72183800	Enhancers	HSMMtube	muscle
46	chr14:72177400-72191200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr14:72178000-72188200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr14:72178000-72190000	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr14:72178000-72190200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr14:72178200-72183400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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