Variant report

Variant	rs8108275
Chromosome Location	chr19:53141566-53141567
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr19:53141440-53141630	K562	blood:	n/a	n/a
2	MXI1	chr19:53141354-53141778	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:53141211-53141921	HepG2	liver:	n/a	n/a
4	MXI1	chr19:53140936-53141747	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:53141041-53141749	K562	blood:	n/a	n/a
6	CHD2	chr19:53141130-53141717	GM12878	blood:	n/a	chr19:53141684-53141694 chr19:53141292-53141302
7	POLR2A	chr19:53140814-53141749	GM12891	blood:	n/a	n/a
8	POLR2A	chr19:53140913-53141864	MCF-7	breast:	n/a	n/a
9	SPI1	chr19:53141164-53141669	GM12891	blood:	n/a	chr19:53141462-53141475
10	POLR2A	chr19:53141141-53141849	K562	blood:	n/a	n/a
11	POLR2A	chr19:53141428-53141653	H1-hESC	embryonic stem cell:	n/a	n/a
12	SIN3AK20	chr19:53141103-53141859	MCF-7	breast:	n/a	n/a
13	POLR2A	chr19:53141209-53141800	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr19:53141058-53141769	K562	blood:	n/a	n/a
15	ELF1	chr19:53141206-53141785	HepG2	liver:	n/a	chr19:53141596-53141607 chr19:53141596-53141607 chr19:53141596-53141605 chr19:53141726-53141738 chr19:53141597-53141606
16	BCLAF1	chr19:53141256-53141655	GM12878	blood:	n/a	chr19:53141336-53141345
17	POLR2A	chr19:53140829-53142173	IMR90	lung:	n/a	n/a
18	RCOR1	chr19:53141415-53141628	HepG2	liver:	n/a	n/a
19	POLR2A	chr19:53140111-53142148	GM12892	blood:	n/a	n/a
20	POLR2A	chr19:53140803-53141852	K562	blood:	n/a	n/a
21	HA-E2F1	chr19:53141080-53141636	MCF-7	breast:	n/a	chr19:53141611-53141620 chr19:53141247-53141259
22	TAF1	chr19:53141312-53141710	K562	blood:	n/a	n/a
23	POLR2A	chr19:53140936-53141762	HUVEC	blood vessel:	n/a	n/a
24	EP300	chr19:53141361-53141606	GM12878	blood:	n/a	chr19:53141514-53141530
25	TAF1	chr19:53141365-53141779	SK-N-SH	brain:	n/a	n/a
26	MAX	chr19:53141065-53141747	K562	blood:	n/a	chr19:53141729-53141739 chr19:53141661-53141671
27	PRDM1	chr19:53141361-53141746	Hela-S3	cervix:	n/a	chr19:53141576-53141585 chr19:53141574-53141589
28	EGR1	chr19:53141489-53141804	K562	blood:	n/a	chr19:53141660-53141670 chr19:53141729-53141739 chr19:53141656-53141669 chr19:53141661-53141671
29	POLR2A	chr19:53141071-53141791	MCF10A-Er-Src	breast:	n/a	n/a
30	PML	chr19:53140972-53141838	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:53140759-53141760	K562	blood:	n/a	n/a
32	TBP	chr19:53141182-53141782	K562	blood:	n/a	n/a
33	NRF1	chr19:53140999-53142488	SK-N-SH	brain:	n/a	chr19:53141607-53141621 chr19:53141729-53141738 chr19:53141610-53141619 chr19:53141661-53141670 chr19:53141610-53141621 chr19:53141610-53141621
34	MAZ	chr19:53141133-53141937	K562	blood:	n/a	chr19:53141729-53141739 chr19:53141661-53141671
35	POLR2A	chr19:53140941-53141840	GM12878	blood:	n/a	n/a
36	POLR2A	chr19:53140938-53142096	K562	blood:	n/a	n/a
37	PML	chr19:53141248-53141694	K562	blood:	n/a	n/a
38	BACH1	chr19:53141538-53141574	K562	blood:	n/a	n/a
39	POLR2A	chr19:53140652-53141971	GM12891	blood:	n/a	n/a
40	SIN3A	chr19:53141008-53142134	H1-hESC	embryonic stem cell:	n/a	chr19:53141199-53141208
41	SPI1	chr19:53141199-53141634	GM12878	blood:	n/a	chr19:53141462-53141475
42	RCOR1	chr19:53141089-53141879	GM12878	blood:	n/a	n/a
43	ZNF143	chr19:53141394-53141594	K562	blood:	n/a	chr19:53141514-53141524
44	HMGN3	chr19:53141179-53141740	K562	blood:	n/a	n/a
45	SP1	chr19:53141252-53142033	GM12878	blood:	n/a	chr19:53141661-53141670 chr19:53141644-53141653 chr19:53141657-53141671 chr19:53141682-53141694 chr19:53141725-53141738 chr19:53141728-53141740 chr19:53141662-53141671 chr19:53141661-53141671 chr19:53141643-53141652 chr19:53141728-53141740 chr19:53141642-53141653 chr19:53141660-53141672 chr19:53141288-53141300 chr19:53141684-53141693 chr19:53141642-53141654 chr19:53141684-53141693 chr19:53141682-53141694 chr19:53141683-53141692 chr19:53141660-53141672 chr19:53141729-53141738 chr19:53141729-53141739 chr19:53141683-53141693 chr19:53141729-53141739 chr19:53141661-53141671 chr19:53141730-53141739 chr19:53141642-53141654
46	MYBL2	chr19:53141284-53141662	HepG2	liver:	n/a	n/a
47	SP4	chr19:53141510-53141891	H1-hESC	embryonic stem cell:	n/a	chr19:53141726-53141742 chr19:53141642-53141653 chr19:53141658-53141674 chr19:53141724-53141740 chr19:53141656-53141672
48	MAX	chr19:53141259-53141693	MCF-7	breast:	n/a	chr19:53141661-53141671
49	JUN	chr19:53141287-53142325	K562	blood:	n/a	chr19:53141559-53141567
50	TBP	chr19:53141166-53141769	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53139623..53144311-chr19:53192220..53194807,4	MCF-7	breast:
2	chr19:53140133..53142689-chr19:53604558..53606639,2	MCF-7	breast:

Variant related genes	Relation type
ZNF83	TF binding region
ENSG00000170949	Chromatin interaction
ENSG00000167766	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11545619	1.00[CEU][hapmap];0.83[GIH][hapmap]
rs11880907	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12971911	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12974376	0.83[EUR][1000 genomes]
rs12974834	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12976870	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12976894	0.93[EUR][1000 genomes]
rs12981759	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13103	0.92[CEU][hapmap];0.83[GIH][hapmap]
rs1903703	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34570404	0.83[EUR][1000 genomes]
rs34721100	0.83[EUR][1000 genomes]
rs34813370	0.83[EUR][1000 genomes]
rs6509661	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs66599469	0.81[EUR][1000 genomes]
rs71358895	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8112866	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv833874	chr19:53058014-53257875	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv912305	chr19:53092465-53349850	Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv912306	chr19:53092465-53400760	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv912307	chr19:53092465-53433054	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv912308	chr19:53092465-53436337	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv912309	chr19:53092465-53440653	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv912310	chr19:53092465-53451291	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv912311	chr19:53103875-53212361	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv912312	chr19:53103875-53296371	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv912313	chr19:53103875-53436337	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
12	nsv912314	chr19:53105547-53144082	Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
13	nsv912315	chr19:53105547-53149967	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
14	nsv912316	chr19:53105547-53158023	Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
15	nsv912317	chr19:53105547-53440653	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
16	nsv1066762	chr19:53112568-53552217	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
17	nsv912318	chr19:53118278-53451291	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
18	nsv458744	chr19:53120559-53236331	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer 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 target site	9 gene(s)	inside rSNPs	diseases
19	nsv580028	chr19:53120559-53236331	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
20	esv3489404	chr19:53121944-53391394	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
21	esv3489405	chr19:53121944-53391394	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
22	nsv1066876	chr19:53123577-53157096	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv580029	chr19:53137583-53164172	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8108275	ZNF83	cis	lymphoblastoid	seeQTL
rs8108275	ZNF83	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53139800-53142000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr19:53140200-53142000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:53140200-53142000	Active TSS	GM12878-XiMat	blood
4	chr19:53140400-53142000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr19:53140400-53142400	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr19:53140400-53142600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:53140600-53141800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:53140600-53142000	Active TSS	H1 Cell Line	embryonic stem cell
9	chr19:53140600-53142000	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr19:53140600-53142000	Active TSS	Rectal Smooth Muscle	rectum
11	chr19:53140600-53142200	Active TSS	H9 Cell Line	embryonic stem cell
12	chr19:53140600-53142200	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr19:53140600-53142200	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr19:53140600-53142200	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr19:53140600-53142400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr19:53140600-53142400	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr19:53140600-53142400	Active TSS	Fetal Kidney	kidney
18	chr19:53140600-53142400	Active TSS	HSMM	muscle
19	chr19:53140800-53141600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr19:53140800-53141600	Active TSS	Placenta Amnion	Placenta Amnion
21	chr19:53140800-53141600	Active TSS	Sigmoid Colon	Sigmoid Colon
22	chr19:53140800-53141800	Active TSS	Primary T cells from cord blood	blood
23	chr19:53140800-53141800	Active TSS	Left Ventricle	heart
24	chr19:53140800-53141800	Active TSS	Small Intestine	intestine
25	chr19:53140800-53142000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr19:53140800-53142000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:53140800-53142000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr19:53140800-53142000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr19:53140800-53142000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr19:53140800-53142000	Active TSS	Fetal Heart	heart
31	chr19:53140800-53142000	Active TSS	Fetal Intestine Large	intestine
32	chr19:53140800-53142000	Active TSS	Gastric	stomach
33	chr19:53140800-53142000	Active TSS	Stomach Mucosa	stomach
34	chr19:53140800-53142000	Active TSS	HepG2	liver
35	chr19:53140800-53142000	Active TSS	NHDF-Ad	bronchial
36	chr19:53140800-53142200	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr19:53140800-53142200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr19:53140800-53142200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr19:53140800-53142200	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr19:53140800-53142200	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr19:53140800-53142200	Active TSS	Aorta	Aorta
42	chr19:53140800-53142200	Active TSS	Fetal Intestine Small	intestine
43	chr19:53140800-53142200	Active TSS	Ovary	ovary
44	chr19:53140800-53142200	Active TSS	Psoas Muscle	Psoas
45	chr19:53140800-53142400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr19:53140800-53142400	Active TSS	Brain Angular Gyrus	brain
47	chr19:53140800-53142400	Active TSS	Brain Substantia Nigra	brain
48	chr19:53140800-53142400	Active TSS	HSMMtube	muscle
49	chr19:53140800-53142400	Active TSS	NHLF	lung
50	chr19:53141000-53141600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--

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