Variant report

Variant	rs221898
Chromosome Location	chr14:71605516-71605517
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:71605350..71606109-chr14:71870362..71870894,2	MCF-7	breast:
2	chr14:71605403..71606379-chr14:72219242..72220271,11	MCF-7	breast:
3	chr14:71605416..71606618-chr14:72219460..72220340,5	MCF-7	breast:
4	chr14:71604707..71606600-chr14:72213499..72215384,2	MCF-7	breast:
5	chr14:71604769..71607668-chr14:71786929..71789620,2	MCF-7	breast:
6	chr14:71605408..71606120-chr14:72322432..72323318,2	K562	blood:

Variant related genes	Relation type
ENSG00000197555	Chromatin interaction
ENSG00000259146	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10132984	0.81[ASN][1000 genomes]
rs10140225	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10140917	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10147068	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10150408	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs116016	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1468470	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1558097	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs221888	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs221889	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs221891	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs221892	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs221893	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs221894	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs221896	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs221900	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs221901	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs221904	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs221906	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs221908	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs221910	0.84[EUR][1000 genomes]
rs221913	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs221914	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs221915	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs221916	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs221917	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs221918	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs221919	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs221924	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs221925	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs221926	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2240531	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2251394	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap]
rs2286311	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2332507	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2526847	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap]
rs2526856	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap]
rs2526859	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2877714	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3784067	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs4132848	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4366661	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs4467005	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.81[ASN][1000 genomes]
rs4531677	0.81[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs4899382	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6573994	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7143595	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs7144986	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7145285	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7152845	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7154395	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7154437	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap]
rs7155247	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7156009	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8005160	0.96[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap]
rs8006046	0.92[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.81[ASN][1000 genomes]
rs8007425	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8008111	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8020480	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8021824	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9323556	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs9323557	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.81[ASN][1000 genomes]
rs9806042	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1035416	chr14:71212882-71623271	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv542126	chr14:71212882-71623271	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv1037839	chr14:71263886-71625114	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv542127	chr14:71263886-71625114	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv1038007	chr14:71269747-71667680	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv565043	chr14:71395604-71625112	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1036929	chr14:71469148-71683412	Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1044090	chr14:71496198-71780026	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs221898	PCNX	cis	Thyroid	GTEx
rs221898	PCNX	cis	parietal	SCAN
rs221898	PCNX	cis	Skin Sun Exposed Lower leg	GTEx
rs221898	PCNX	cis	Nerve Tibial	GTEx
rs221898	PCNX	cis	Artery Tibial	GTEx
rs221898	ZFYVE1	cis	cerebellum	SCAN
rs221898	HEATR4	cis	cerebellum	SCAN
rs221898	PCNX	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71597400-71605600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr14:71598400-71608600	Weak transcription	NHLF	lung
3	chr14:71604400-71606400	Enhancers	NH-A	brain
4	chr14:71604600-71608400	Weak transcription	Spleen	Spleen
5	chr14:71604800-71605600	Enhancers	Osteobl	bone
6	chr14:71605000-71605600	Enhancers	NHDF-Ad	bronchial
7	chr14:71605000-71605800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr14:71605000-71605800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr14:71605200-71605600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr14:71605200-71605600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr14:71605200-71605800	Enhancers	Fetal Brain Female	brain
12	chr14:71605200-71605800	Enhancers	HMEC	breast
13	chr14:71605200-71606200	Enhancers	NHEK	skin
14	chr14:71605200-71606400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr14:71605200-71606400	Enhancers	Hela-S3	cervix
16	chr14:71605400-71605600	Enhancers	Brain Anterior Caudate	brain
17	chr14:71605400-71605600	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr14:71605400-71605800	Enhancers	Brain Cingulate Gyrus	brain
19	chr14:71605400-71605800	Enhancers	Brain Hippocampus Middle	brain
20	chr14:71605400-71606000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr14:71605400-71606000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr14:71605400-71606000	Enhancers	Fetal Heart	heart
23	chr14:71605400-71606200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr14:71605400-71606200	Enhancers	Brain Substantia Nigra	brain
25	chr14:71605400-71606200	Enhancers	Fetal Brain Male	brain
26	chr14:71605400-71606600	Enhancers	HUES6 Cell Line	embryonic stem cell

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