Variant report

Variant	rs2891577
Chromosome Location	chr19:55914444-55914445
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:44)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:44 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:55913064-55914514	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:55913745-55914763	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr19:55914309-55914487	A549	lung:	n/a	n/a
4	POLR2A	chr19:55914315-55914535	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr19:55910031-55914597	GM12892	blood:	n/a	n/a
6	POLR2A	chr19:55913119-55914513	K562	blood:	n/a	n/a
7	POLR2A	chr19:55913029-55914640	K562	blood:	n/a	n/a
8	POLR2A	chr19:55913162-55915007	GM12891	blood:	n/a	n/a
9	POLR2A	chr19:55913163-55914553	K562	blood:	n/a	n/a
10	POLR2A	chr19:55913129-55914598	K562	blood:	n/a	n/a
11	POLR2A	chr19:55913207-55914571	K562	blood:	n/a	n/a
12	POLR2A	chr19:55913609-55914596	GM12892	blood:	n/a	n/a
13	POLR2A	chr19:55913117-55914634	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:55913211-55914603	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr19:55909545-55914730	U87	brain:	n/a	n/a
16	POLR2A	chr19:55913648-55914552	A549	lung:	n/a	n/a
17	HEY1	chr19:55911616-55914690	K562	blood:	n/a	n/a
18	POLR2A	chr19:55914246-55914557	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr19:55912876-55915088	K562	blood:	n/a	n/a
20	POLR2A	chr19:55913628-55914532	MCF-7	breast:	n/a	n/a
21	POLR2A	chr19:55910121-55915188	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:55914308-55914468	A549	lung:	n/a	n/a
23	POLR2A	chr19:55913100-55914657	K562	blood:	n/a	n/a
24	POLR2A	chr19:55912696-55914881	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr19:55913426-55914825	GM12892	blood:	n/a	n/a
26	POLR2A	chr19:55910669-55914680	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr19:55910140-55916359	PFSK-1	brain:	n/a	n/a
28	POLR2A	chr19:55914313-55914847	HCT-116	colon:	n/a	n/a
29	POLR2A	chr19:55909693-55915034	U87	brain:	n/a	n/a
30	POLR2A	chr19:55913041-55914763	K562	blood:	n/a	n/a
31	POLR2A	chr19:55913172-55914911	K562	blood:	n/a	n/a
32	POLR2A	chr19:55914428-55914946	PANC-1	pancreas:	n/a	n/a
33	POLR2A	chr19:55914300-55914531	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr19:55914305-55914513	A549	lung:	n/a	n/a
35	POLR2A	chr19:55910731-55915070	GM12878	blood:	n/a	n/a
36	POLR2A	chr19:55913078-55914571	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr19:55913705-55914462	HL-60	blood:	n/a	n/a
38	POLR2A	chr19:55913051-55915003	A549	lung:	n/a	n/a
39	POLR2A	chr19:55913142-55914511	K562	blood:	n/a	n/a
40	POLR2A	chr19:55914369-55914477	HepG2	liver:	n/a	n/a
41	POLR2A	chr19:55912808-55914489	GM12891	blood:	n/a	n/a
42	POLR2A	chr19:55913961-55914509	HepG2	liver:	n/a	n/a
43	HEY1	chr19:55914252-55914537	K562	blood:	n/a	n/a
44	POLR2A	chr19:55910001-55915059	SK-N-MC	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55790204..55793295-chr19:55914436..55917425,4	K562	blood:
2	chr19:55766579..55768954-chr19:55914081..55916884,2	K562	blood:
3	chr19:55913931..55915922-chr19:55972282..55974856,2	MCF-7	breast:
4	chr19:55857803..55861096-chr19:55912151..55914962,3	K562	blood:
5	chr19:55865344..55867006-chr19:55913692..55915275,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267093	TF binding region
ENSG00000105063	Chromatin interaction
ENSG00000133265	Chromatin interaction
ENSG00000160471	Chromatin interaction
ENSG00000063241	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10403361	0.92[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10414353	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10426501	0.83[CHD][hapmap]
rs1124917	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12460492	1.00[ASN][1000 genomes]
rs12462594	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12977195	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12977341	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12979229	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12979256	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12985701	0.92[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13343706	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16986359	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28411209	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28454071	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28635028	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73606242	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73619625	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
2	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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 miRNA target site	228 gene(s)	inside rSNPs	diseases
4	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
5	nsv912462	chr19:55845386-55925500	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
6	nsv912463	chr19:55845386-56004901	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
7	nsv912464	chr19:55850269-55921164	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
8	nsv912465	chr19:55854313-55935184	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
9	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2891577	RPL28	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55900200-55918400	Weak transcription	Psoas Muscle	Psoas
2	chr19:55900600-55917600	Weak transcription	Stomach Mucosa	stomach
3	chr19:55901000-55917800	Weak transcription	Right Atrium	heart
4	chr19:55901800-55916800	Weak transcription	Fetal Brain Male	brain
5	chr19:55902200-55917400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:55910200-55917000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr19:55910800-55917200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:55910800-55917600	Strong transcription	Brain Anterior Caudate	brain
9	chr19:55911000-55915400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr19:55911000-55915800	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr19:55911000-55917000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr19:55911000-55917000	Strong transcription	Primary B cells from peripheral blood	blood
13	chr19:55911000-55917000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr19:55911000-55917000	Strong transcription	Fetal Intestine Large	intestine
15	chr19:55911000-55917000	Strong transcription	Stomach Smooth Muscle	stomach
16	chr19:55911200-55914600	Strong transcription	Osteobl	bone
17	chr19:55911200-55915400	Strong transcription	Fetal Thymus	thymus
18	chr19:55911200-55915800	Strong transcription	Primary T cells from cord blood	blood
19	chr19:55911200-55916800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:55911200-55917000	Strong transcription	Fetal Stomach	stomach
21	chr19:55911200-55917200	Strong transcription	Brain Hippocampus Middle	brain
22	chr19:55911400-55915400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr19:55911400-55916000	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr19:55911400-55916800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:55911400-55917000	Strong transcription	Duodenum Mucosa	Duodenum
26	chr19:55911600-55915400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:55911600-55915400	Genic enhancers	A549	lung
28	chr19:55911600-55916000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr19:55911600-55916200	Strong transcription	Placenta Amnion	Placenta Amnion
30	chr19:55911600-55916600	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr19:55911600-55916600	Strong transcription	NH-A	brain
32	chr19:55911600-55916800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:55911600-55916800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:55911600-55917000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr19:55911600-55917000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr19:55911600-55917000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr19:55911800-55914600	Strong transcription	HUVEC	blood vessel
38	chr19:55911800-55915000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr19:55911800-55915000	Strong transcription	Right Ventricle	heart
40	chr19:55911800-55915400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:55911800-55915400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr19:55911800-55915400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr19:55911800-55915400	Strong transcription	Spleen	Spleen
44	chr19:55911800-55915600	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr19:55911800-55915600	Strong transcription	NHLF	lung
46	chr19:55911800-55915800	Strong transcription	Primary hematopoietic stem cells	blood
47	chr19:55911800-55916000	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr19:55911800-55916000	Strong transcription	Liver	Liver
49	chr19:55911800-55916200	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr19:55911800-55916200	Strong transcription	Ovary	ovary

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