Variant report

Variant	rs6819857
Chromosome Location	chr4:771587-771588
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:644153..646980-chr4:769830..771773,2	K562	blood:
2	chr4:697549..703820-chr4:770860..775722,9	K562	blood:
3	chr4:758084..763800-chr4:770671..778725,12	MCF-7	breast:
4	chr4:770559..774303-chr4:822047..825549,3	MCF-7	breast:
5	chr4:770677..772460-chr4:828293..831187,2	MCF-7	breast:
6	chr4:698737..701274-chr4:771088..772806,3	K562	blood:
7	chr4:664408..666949-chr4:770697..772344,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260262	Chromatin interaction
ENSG00000185619	Chromatin interaction
ENSG00000133256	Chromatin interaction
ENSG00000233799	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11931963	0.80[LWK][hapmap];0.89[MKK][hapmap]
rs11934187	0.84[AFR][1000 genomes]
rs11936723	0.84[AFR][1000 genomes]
rs13105255	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13105473	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13105702	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13122480	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13131168	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13131185	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13136722	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13147679	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13151247	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1564279	0.80[CEU][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs2242237	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28497436	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34959417	0.80[ASN][1000 genomes]
rs35333201	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4234854	0.85[ASN][1000 genomes]
rs6811216	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6811804	0.89[LWK][hapmap];0.81[AFR][1000 genomes]
rs6838241	0.87[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.85[ASN][1000 genomes]
rs6840352	0.89[LWK][hapmap];0.85[MKK][hapmap]
rs7336	0.80[LWK][hapmap];0.89[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:27 , 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	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
19	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
20	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
21	nsv520136	chr4:759709-780883	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
22	nsv1003219	chr4:769894-1105464	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
23	nsv515844	chr4:771587-780883	Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
24	nsv526780	chr4:771587-786401	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
25	nsv521402	chr4:771587-793763	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
26	nsv878262	chr4:771587-865227	Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
27	nsv878263	chr4:771587-1047794	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6819857	PCGF3	cis	Artery Tibial	GTEx
rs6819857	CPLX1	cis	Thyroid	GTEx
rs6819857	CPLX1	cis	Esophagus Muscularis	GTEx
rs6819857	AC139887.4	cis	Artery Tibial	GTEx
rs6819857	RP11-440L14.1	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:746000-773800	Weak transcription	Fetal Brain Male	brain
2	chr4:753600-773800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:753800-771600	Strong transcription	Primary B cells from peripheral blood	blood
4	chr4:753800-773200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:753800-773200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr4:753800-773400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr4:753800-773400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr4:754000-771600	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr4:754000-773600	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr4:754200-771600	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr4:754400-773400	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:755600-774200	Weak transcription	Hela-S3	cervix
13	chr4:758400-774200	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr4:758600-773800	Strong transcription	Fetal Thymus	thymus
15	chr4:759600-773800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr4:759800-773400	Strong transcription	NHLF	lung
17	chr4:761000-773000	Strong transcription	Fetal Intestine Large	intestine
18	chr4:761400-774200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:761800-774200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr4:762000-773400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:762000-773400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:762200-773400	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr4:762400-773400	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr4:762600-773400	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr4:762800-774000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr4:764200-774200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr4:764800-773400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:765200-774000	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr4:765400-771600	Genic enhancers	Brain Anterior Caudate	brain
30	chr4:766600-771600	Genic enhancers	Primary T cells fromperipheralblood	blood
31	chr4:766600-771600	Genic enhancers	Lung	lung
32	chr4:766600-773800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr4:766800-771600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr4:766800-772200	Strong transcription	Fetal Brain Female	brain
35	chr4:766800-773400	Strong transcription	HUVEC	blood vessel
36	chr4:767200-773400	Strong transcription	HSMM	muscle
37	chr4:767600-772800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr4:767600-772800	Strong transcription	Placenta	Placenta
39	chr4:767600-773000	Weak transcription	Stomach Mucosa	stomach
40	chr4:767800-771600	Strong transcription	Esophagus	oesophagus
41	chr4:767800-773200	Strong transcription	Fetal Muscle Trunk	muscle
42	chr4:768000-773000	Strong transcription	Fetal Lung	lung
43	chr4:768000-773400	Strong transcription	NHEK	skin
44	chr4:768000-773600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
45	chr4:768200-771600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr4:768200-773400	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr4:768200-773600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr4:768200-773800	Strong transcription	Osteobl	bone
49	chr4:768200-774200	Genic enhancers	Brain Inferior Temporal Lobe	brain
50	chr4:768400-772000	Strong transcription	Primary hematopoietic stem cells	blood

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