Variant report

Variant	rs12979058
Chromosome Location	chr19:35750684-35750685
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	POLR2A	chr19:35750586-35751099	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr19:35750532-35751035	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr19:35750565-35750998	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:35750525-35751048	K562	blood:	n/a	n/a
5	POLR2A	chr19:35750570-35751026	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr19:35750649-35750966	HepG2	liver:	n/a	n/a
7	POLR2A	chr19:35750626-35750990	A549	lung:	n/a	n/a
8	POLR2A	chr19:35750440-35751081	GM12892	blood:	n/a	n/a
9	POLR2A	chr19:35750515-35751171	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr19:35750573-35750947	MCF-7	breast:	n/a	n/a
11	POLR2A	chr19:35748057-35751220	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr19:35750443-35751093	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr19:35750433-35750983	HepG2	liver:	n/a	n/a
14	POLR2A	chr19:35750517-35751005	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:35750597-35751030	A549	lung:	n/a	n/a
16	POLR2A	chr19:35749343-35751113	K562	blood:	n/a	n/a
17	POLR2A	chr19:35750517-35751082	H1-neurons	neurons:	n/a	n/a
18	POLR2A	chr19:35750436-35751137	GM12892	blood:	n/a	n/a
19	POLR2A	chr19:35750559-35751058	MCF10A-Er-Src	breast:	n/a	n/a
20	BCL3	chr19:35750498-35750783	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:35749531-35751167	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr19:35748030-35751131	K562	blood:	n/a	n/a
23	POLR2A	chr19:35750625-35751065	A549	lung:	n/a	n/a
24	POLR2A	chr19:35750454-35751138	MCF-7	breast:	n/a	n/a
25	POLR2A	chr19:35750613-35750927	HCT-116	colon:	n/a	n/a
26	POLR2A	chr19:35750429-35751099	GM12878	blood:	n/a	n/a
27	POLR2A	chr19:35750581-35751026	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000268947	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10405246	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10410675	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10414846	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10419261	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10419959	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10421096	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10421504	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10421599	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10421768	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10424619	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1051995	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1052033	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12973672	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12974791	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12975284	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12979792	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12981527	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12984022	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12985618	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12986033	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13345192	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2073899	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2280744	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2280745	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2280747	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28365133	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28365136	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34832786	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35250673	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35497966	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35959789	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62109572	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62112772	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71352913	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7256866	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8101606	0.85[EUR][1000 genomes];0.89[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	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS 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	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv510765	chr19:35708226-35890668	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	esv2758497	chr19:35711078-35887113	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	esv2758758	chr19:35711078-35887113	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv911618	chr19:35734107-35807845	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
8	esv1836312	chr19:35741456-35786868	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	n/a
9	nsv911619	chr19:35749563-35775441	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' 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	n/a

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35741200-35758000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:35741400-35757800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:35742000-35756200	Strong transcription	NHEK	skin
4	chr19:35742600-35755200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:35743800-35756600	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr19:35744400-35757600	Strong transcription	Fetal Intestine Large	intestine
7	chr19:35744600-35752400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr19:35744600-35752600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr19:35744800-35757600	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr19:35744800-35757600	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr19:35744800-35757800	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr19:35744800-35758000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr19:35745000-35757800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr19:35746000-35751600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:35746000-35752400	Weak transcription	Right Ventricle	heart
16	chr19:35746200-35755200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr19:35746600-35755000	Weak transcription	GM12878-XiMat	blood
18	chr19:35746600-35757600	Strong transcription	Fetal Intestine Small	intestine
19	chr19:35746600-35757600	Weak transcription	Hela-S3	cervix
20	chr19:35746800-35752000	Enhancers	Liver	Liver
21	chr19:35746800-35752400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr19:35746800-35756000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:35747600-35755200	Weak transcription	Fetal Heart	heart
24	chr19:35747800-35755400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr19:35747800-35755600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr19:35748400-35756000	Strong transcription	Duodenum Mucosa	Duodenum
27	chr19:35748600-35752400	Weak transcription	Stomach Mucosa	stomach
28	chr19:35748800-35756600	Weak transcription	Primary T cells from cord blood	blood
29	chr19:35748800-35757600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr19:35749000-35750800	Strong transcription	Gastric	stomach
31	chr19:35749000-35752000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr19:35749000-35752000	Weak transcription	Lung	lung
33	chr19:35749000-35752200	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr19:35749000-35752200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr19:35749000-35752400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:35749000-35752600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr19:35749000-35752600	Weak transcription	Placenta	Placenta
38	chr19:35749000-35753000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr19:35749000-35753800	Strong transcription	Esophagus	oesophagus
40	chr19:35749000-35755000	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr19:35749000-35756000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr19:35749000-35756200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr19:35749000-35756600	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr19:35749000-35757000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr19:35749000-35758000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr19:35749200-35753800	Strong transcription	HepG2	liver
47	chr19:35749200-35754000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr19:35749200-35756200	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr19:35749200-35756600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr19:35749400-35757600	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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