Variant report

Variant	rs2926748
Chromosome Location	chr12:57109412-57109413
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57109382-57110822	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr12:57109108-57110760	HL-60	blood:	n/a	n/a
3	POLR2A	chr12:57109219-57110872	GM12892	blood:	n/a	n/a
4	POLR2A	chr12:57109163-57109636	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr12:57109223-57113587	K562	blood:	n/a	n/a
6	POLR2A	chr12:57109373-57115069	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr12:57109205-57109741	K562	blood:	n/a	n/a
8	POLR2A	chr12:57109177-57115890	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr12:57109197-57110693	HepG2	liver:	n/a	n/a
10	POLR2A	chr12:57109238-57110415	GM12891	blood:	n/a	n/a
11	POLR2A	chr12:57109046-57111519	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr12:57109230-57111658	K562	blood:	n/a	n/a
13	POLR2A	chr12:57109283-57116293	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:57109120-57109917	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr12:57109278-57110564	MCF-7	breast:	n/a	n/a
16	POLR2A	chr12:57109342-57110329	HepG2	liver:	n/a	n/a
17	POLR2A	chr12:57109094-57117058	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr12:57109165-57110714	GM12892	blood:	n/a	n/a
19	POLR2A	chr12:57109115-57110514	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr12:57109250-57110612	A549	lung:	n/a	n/a
21	POLR2A	chr12:57108026-57111457	HepG2	liver:	n/a	n/a
22	POLR2A	chr12:57109291-57111137	K562	blood:	n/a	n/a
23	POLR2A	chr12:57109356-57117115	GM12878	blood:	n/a	n/a
24	POLR2A	chr12:57109353-57111565	HL-60	blood:	n/a	n/a
25	POLR2A	chr12:57109111-57113222	GM12892	blood:	n/a	n/a
26	POLR2A	chr12:57108774-57111413	K562	blood:	n/a	n/a
27	POLR2A	chr12:57109233-57116354	PANC-1	pancreas:	n/a	n/a
28	POLR2A	chr12:57109407-57110580	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57078008..57083064-chr12:57107591..57112002,6	MCF-7	breast:
2	chr12:57025967..57028369-chr12:57109076..57111615,2	K562	blood:
3	chr12:57074578..57085543-chr12:57108746..57121559,55	K562	blood:
4	chr12:57029529..57031708-chr12:57108822..57111712,2	K562	blood:
5	chr12:57079048..57083970-chr12:57107938..57112602,6	K562	blood:
6	chr12:57098172..57100413-chr12:57108972..57110548,2	MCF-7	breast:

No data

Variant related genes	Relation type
NACA	TF binding region
ENSG00000110958	Chromatin interaction
ENSG00000076108	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1026565	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10459246	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10747769	0.83[EUR][1000 genomes]
rs10747770	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783796	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876916	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10876918	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11171951	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171956	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1131514	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12227117	0.82[ASN][1000 genomes]
rs12828563	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1466382	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563896	0.83[ASN][1000 genomes]
rs1563897	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1975875	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1979325	0.97[ASN][1000 genomes]
rs2035081	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2035082	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290893	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2290894	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2926741	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2926743	0.97[ASN][1000 genomes]
rs2926747	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2958127	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2958130	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2958132	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2958134	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2958148	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2958149	0.94[ASN][1000 genomes]
rs2958153	0.81[ASN][1000 genomes]
rs2958155	0.80[EUR][1000 genomes]
rs3214051	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4759256	0.90[ASN][1000 genomes]
rs4788	0.96[ASN][1000 genomes]
rs4902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137749	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7295862	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7297289	0.80[ASN][1000 genomes]
rs7303216	0.80[ASN][1000 genomes]
rs7313074	0.90[ASN][1000 genomes]
rs7966391	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7967600	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7978685	0.96[ASN][1000 genomes]
rs7980317	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7980835	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs898609	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898611	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9989034	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer 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	181 gene(s)	inside rSNPs	diseases
2	nsv559016	chr12:57095815-57112637	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57089000-57109600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:57104000-57114600	Weak transcription	Fetal Brain Male	brain
3	chr12:57104600-57109800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:57104600-57110200	Strong transcription	Fetal Stomach	stomach
5	chr12:57104600-57112600	Strong transcription	Fetal Intestine Large	intestine
6	chr12:57104600-57115000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:57104800-57109600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:57104800-57109600	Strong transcription	Liver	Liver
9	chr12:57104800-57109600	Strong transcription	Fetal Muscle Leg	muscle
10	chr12:57104800-57109600	Strong transcription	NH-A	brain
11	chr12:57104800-57109800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:57104800-57109800	Strong transcription	Muscle Satellite Cultured Cells	--
13	chr12:57104800-57110000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:57104800-57110000	Strong transcription	Brain Germinal Matrix	brain
15	chr12:57104800-57110000	Strong transcription	Stomach Smooth Muscle	stomach
16	chr12:57104800-57110000	Strong transcription	A549	lung
17	chr12:57104800-57110200	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr12:57104800-57110200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr12:57104800-57110200	Strong transcription	Placenta	Placenta
20	chr12:57104800-57110400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr12:57104800-57110600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr12:57104800-57110600	Strong transcription	Osteobl	bone
23	chr12:57104800-57111000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:57104800-57111200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:57104800-57111200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:57104800-57111200	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr12:57104800-57111200	Strong transcription	HSMM	muscle
28	chr12:57104800-57111400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:57105000-57109600	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr12:57105000-57109600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:57105000-57109600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:57105000-57109600	Strong transcription	Adipose Nuclei	Adipose
33	chr12:57105000-57109600	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr12:57105000-57109600	Strong transcription	HUVEC	blood vessel
35	chr12:57105000-57109800	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr12:57105000-57109800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:57105000-57109800	Strong transcription	Fetal Muscle Trunk	muscle
38	chr12:57105000-57110000	Strong transcription	Primary B cells from cord blood	blood
39	chr12:57105000-57110200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr12:57105000-57110200	Strong transcription	Dnd41	blood
41	chr12:57105000-57110400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr12:57105000-57110400	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr12:57105000-57110600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr12:57105000-57110600	Strong transcription	HepG2	liver
45	chr12:57105000-57110600	Strong transcription	NHDF-Ad	bronchial
46	chr12:57105000-57110800	Strong transcription	Duodenum Mucosa	Duodenum
47	chr12:57105000-57111200	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr12:57105000-57111400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
49	chr12:57105000-57111600	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr12:57105200-57109600	Strong transcription	Primary T cells fromperipheralblood	blood

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