Variant report

Variant	rs221893
Chromosome Location	chr14:71611414-71611415
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71610357..71611926-chr14:71786839..71789393,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259146	Chromatin interaction
ENSG00000197555	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10140225	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs10140917	0.81[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap]
rs10147068	0.81[ASN][1000 genomes]
rs10150408	0.81[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs116016	0.81[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1468470	0.80[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1558097	0.80[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs221888	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs221889	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs221891	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs221892	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs221894	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs221896	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs221898	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]
rs221900	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs221901	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs221904	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs221906	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs221908	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs221913	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs221914	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs221915	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs221916	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs221917	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs221918	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs221919	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs221924	0.83[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs221925	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs221926	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2240531	0.83[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2251394	0.83[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap]
rs2286311	0.80[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2332507	0.81[ASN][1000 genomes]
rs2526847	0.83[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap]
rs2526856	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs2526859	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs2877714	0.83[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3784067	0.80[CEU][hapmap];0.94[JPT][hapmap]
rs4132848	0.80[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs4366661	0.83[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap]
rs4467005	0.83[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs4531677	0.94[JPT][hapmap]
rs4899382	1.00[JPT][hapmap]
rs6573994	0.80[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7143595	0.80[CEU][hapmap];0.83[CHB][hapmap]
rs7144986	0.81[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs7145285	0.81[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7152845	0.83[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs7154395	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7154437	0.83[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs7155247	1.00[JPT][hapmap]
rs7156009	0.83[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap]
rs8005160	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs8006046	0.83[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap]
rs8007425	0.80[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs8008111	0.81[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs8020480	0.83[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap]
rs8021824	0.80[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs9323556	0.81[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs9323557	0.83[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs9806042	0.80[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs221893	PCNX	cis	Nerve Tibial	GTEx
rs221893	PCNX	cis	Artery Tibial	GTEx
rs221893	PCNX	cis	Adipose Subcutaneous	GTEx
rs221893	PCNX	Cis_1M	lymphoblastoid	RTeQTL
rs221893	PCNX	cis	Skin Sun Exposed Lower leg	GTEx
rs221893	PCNX	cis	Thyroid	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71605600-71613200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr14:71605600-71613400	Enhancers	Placenta	Placenta
3	chr14:71606600-71614800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr14:71609800-71613000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr14:71610000-71613200	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr14:71610200-71615000	Weak transcription	Fetal Thymus	thymus
7	chr14:71610400-71611800	Enhancers	Hela-S3	cervix
8	chr14:71610400-71612000	Weak transcription	Spleen	Spleen
9	chr14:71610600-71615200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr14:71610600-71615400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr14:71610800-71612200	Weak transcription	HepG2	liver
12	chr14:71610800-71612400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr14:71610800-71613000	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr14:71610800-71613400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr14:71610800-71613800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr14:71610800-71615400	Weak transcription	Primary T cells from cord blood	blood
17	chr14:71610800-71615400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr14:71610800-71615400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr14:71611000-71611600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr14:71611000-71615000	Weak transcription	Dnd41	blood

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