Variant report

Variant	rs1204992
Chromosome Location	chr14:72198511-72198512
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1005605	0.94[ASN][1000 genomes]
rs10132111	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10133626	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10137642	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10139519	1.00[JPT][hapmap]
rs1204988	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1204995	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1204996	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1204997	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12880188	1.00[JPT][hapmap]
rs1468373	0.94[ASN][1000 genomes]
rs1981588	1.00[JPT][hapmap]
rs2286135	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2286136	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3784064	1.00[JPT][hapmap]
rs3825719	1.00[JPT][hapmap]
rs4140799	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4899398	1.00[JPT][hapmap]
rs7140501	1.00[JPT][hapmap]
rs7142343	1.00[JPT][hapmap]
rs7156313	1.00[JPT][hapmap]
rs7350725	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs757744	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8015004	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9672060	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1204992	PCNX	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72148200-72200400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr14:72160200-72202000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr14:72165200-72202000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr14:72168800-72201600	Weak transcription	Stomach Mucosa	stomach
5	chr14:72176400-72200000	Weak transcription	Small Intestine	intestine
6	chr14:72182200-72207400	Strong transcription	GM12878-XiMat	blood
7	chr14:72185800-72206200	Strong transcription	Primary B cells from peripheral blood	blood
8	chr14:72187000-72204000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr14:72187600-72206200	Strong transcription	Dnd41	blood
10	chr14:72187600-72207600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr14:72187800-72206200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr14:72188200-72206400	Strong transcription	Primary T cells from cord blood	blood
13	chr14:72188600-72206000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr14:72188800-72199400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr14:72188800-72205800	Strong transcription	Fetal Intestine Large	intestine
16	chr14:72188800-72207600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr14:72189600-72204400	Strong transcription	Fetal Stomach	stomach
18	chr14:72189800-72205800	Strong transcription	Fetal Intestine Small	intestine
19	chr14:72189800-72206000	Strong transcription	Duodenum Mucosa	Duodenum
20	chr14:72189800-72206000	Strong transcription	Spleen	Spleen
21	chr14:72189800-72206600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr14:72189800-72206800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr14:72189800-72206800	Strong transcription	Primary B cells from cord blood	blood
24	chr14:72190000-72206000	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr14:72190000-72206000	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr14:72190200-72206000	Strong transcription	Placenta	Placenta
27	chr14:72190600-72214200	Weak transcription	K562	blood
28	chr14:72191400-72206000	Strong transcription	Liver	Liver
29	chr14:72191600-72206000	Strong transcription	Gastric	stomach
30	chr14:72191600-72206000	Strong transcription	Pancreas	Pancrea
31	chr14:72192400-72202000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr14:72193000-72207200	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr14:72193400-72204000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr14:72193800-72204400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr14:72194000-72199400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr14:72194000-72199400	Weak transcription	NHDF-Ad	bronchial
37	chr14:72194000-72199800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr14:72194200-72199000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr14:72194200-72204200	Weak transcription	Fetal Brain Male	brain
40	chr14:72194200-72204400	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr14:72194600-72214800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr14:72194800-72203600	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr14:72195000-72205400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr14:72195000-72206400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr14:72195200-72205600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr14:72195200-72206000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr14:72195200-72206000	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr14:72195200-72206600	Strong transcription	Thymus	Thymus
49	chr14:72195400-72206000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr14:72195800-72204200	Strong transcription	Brain Inferior Temporal Lobe	brain

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