Variant report

Variant	rs899393
Chromosome Location	chr4:758366-758367
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:725258..728014-chr4:756169..758632,2	MCF-7	breast:
2	chr4:758084..763800-chr4:770671..778725,12	MCF-7	breast:
3	chr4:757903..760151-chr4:923832..926606,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CPLX1-3	chr4:758275-758397	ENSG00000233799.1

Variant related genes	Relation type
ENSG00000178950	Chromatin interaction
ENSG00000249592	Chromatin interaction
ENSG00000127419	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11248040	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11723514	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11724278	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11725571	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11729160	0.81[AMR][1000 genomes]
rs11729987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11734005	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13127733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17165032	0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs17165034	0.92[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2242233	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3733358	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3775143	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4690194	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4690281	1.00[ASW][hapmap];0.85[CEU][hapmap];0.85[LWK][hapmap];0.88[MKK][hapmap];0.81[TSI][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes]
rs4690282	0.81[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4690307	0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4690310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4690311	0.91[ASN][1000 genomes]
rs4690312	0.90[ASN][1000 genomes]
rs4690315	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57170954	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59438465	0.91[AFR][1000 genomes]
rs60018246	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73207757	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7682244	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs899391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
5	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
9	esv1829397	chr4:655939-1041957	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
10	nsv829834	chr4:665477-775524	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
11	nsv878253	chr4:708932-771587	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	nsv878254	chr4:708932-899143	Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv878255	chr4:708932-1052488	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
14	nsv878257	chr4:712222-852313	Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv878258	chr4:712222-1058358	Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
16	nsv878259	chr4:713920-852313	Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
17	nsv878260	chr4:713920-1052488	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv4195	chr4:727187-768059	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
19	nsv966467	chr4:744990-760620	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
20	nsv818207	chr4:753944-821490	Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
21	nsv878261	chr4:756686-1047794	Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
22	nsv1007928	chr4:757263-813885	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs899393	PCGF3	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:727000-767600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:728600-763400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr4:729000-762600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr4:729600-760800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr4:742600-763600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr4:742800-764000	Weak transcription	Small Intestine	intestine
7	chr4:744400-763400	Weak transcription	Right Atrium	heart
8	chr4:746000-773800	Weak transcription	Fetal Brain Male	brain
9	chr4:746200-758600	Weak transcription	Brain Anterior Caudate	brain
10	chr4:748200-763400	Weak transcription	Brain Substantia Nigra	brain
11	chr4:753600-759400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:753600-759400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr4:753600-769000	ZNF genes & repeats	Fetal Stomach	stomach
14	chr4:753600-773800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:753800-758600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:753800-758600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:753800-758600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:753800-759200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:753800-759200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:753800-759400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:753800-759600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
22	chr4:753800-759800	Strong transcription	GM12878-XiMat	blood
23	chr4:753800-761000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:753800-761000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:753800-761400	Strong transcription	Colonic Mucosa	Colon
26	chr4:753800-764200	ZNF genes & repeats	Aorta	Aorta
27	chr4:753800-764600	Strong transcription	Fetal Muscle Leg	muscle
28	chr4:753800-764800	Strong transcription	Fetal Lung	lung
29	chr4:753800-765400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr4:753800-766600	Strong transcription	Dnd41	blood
31	chr4:753800-768000	Strong transcription	Thymus	Thymus
32	chr4:753800-768400	Strong transcription	Primary T cells from cord blood	blood
33	chr4:753800-771600	Strong transcription	Primary B cells from peripheral blood	blood
34	chr4:753800-773200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr4:753800-773200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:753800-773400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr4:753800-773400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr4:754000-758800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr4:754000-761400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:754000-764000	Strong transcription	Fetal Brain Female	brain
41	chr4:754000-771600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr4:754000-773600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr4:754200-758400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr4:754200-758400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:754200-759400	Strong transcription	NHLF	lung
46	chr4:754200-765200	Strong transcription	Ovary	ovary
47	chr4:754200-765600	Strong transcription	Duodenum Mucosa	Duodenum
48	chr4:754200-765600	Strong transcription	Gastric	stomach
49	chr4:754200-771600	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr4:754400-758400	Strong transcription	ES-I3 Cell Line	embryonic stem cell

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