Variant report

Variant	rs2107670
Chromosome Location	chr14:71634867-71634868
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71630664..71636301-chr14:71785635..71788811,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197555	Chromatin interaction
ENSG00000259146	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11849257	0.93[EUR][1000 genomes]
rs12323786	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2332536	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28406336	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56022326	0.84[ASN][1000 genomes]
rs61989172	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61989176	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61992087	0.81[ASN][1000 genomes]
rs8005045	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8018758	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	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
5	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2107670	PCNX	Cis_1M	lymphoblastoid	RTeQTL
rs2107670	PCNX	cis	Artery Tibial	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71631600-71636600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr14:71631800-71636600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr14:71632200-71636600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr14:71632600-71635200	Weak transcription	Right Atrium	heart
5	chr14:71633000-71635000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr14:71633400-71648000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr14:71633600-71635000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr14:71633600-71639200	Weak transcription	Fetal Lung	lung
9	chr14:71633800-71636600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr14:71634600-71648200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr14:71634800-71635000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr14:71634800-71635000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr14:71634800-71635000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr14:71634800-71635000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr14:71634800-71635000	Flanking Active TSS	Dnd41	blood
16	chr14:71634800-71635200	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr14:71634800-71635200	Active TSS	Primary hematopoietic stem cells	blood
18	chr14:71634800-71635200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr14:71634800-71635400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr14:71634800-71635400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr14:71634800-71635400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr14:71634800-71635400	Active TSS	Monocytes-CD14+_RO01746	blood
23	chr14:71634800-71635600	Active TSS	Primary T cells from cord blood	blood
24	chr14:71634800-71635800	Flanking Active TSS	Primary T cells fromperipheralblood	blood

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