Variant report

Variant	rs2926747
Chromosome Location	chr12:57109931-57109932
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:52)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:52 , 50 per page) page: 1 2

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	chr12:57109223-57113587	K562	blood:	n/a	n/a
5	POLR2A	chr12:57109373-57115069	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr12:57109473-57110293	GM12891	blood:	n/a	n/a
7	POLR2A	chr12:57109486-57115298	Hela-S3	cervix:	n/a	n/a
8	MTA3	chr12:57109628-57110229	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:57109459-57110558	GM12891	blood:	n/a	n/a
10	POLR2A	chr12:57109818-57110030	A549	lung:	n/a	n/a
11	POLR2A	chr12:57109177-57115890	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr12:57109444-57110590	GM12891	blood:	n/a	n/a
13	POLR2A	chr12:57109197-57110693	HepG2	liver:	n/a	n/a
14	POLR2A	chr12:57109238-57110415	GM12891	blood:	n/a	n/a
15	POLR2A	chr12:57109046-57111519	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr12:57109930-57110637	K562	blood:	n/a	n/a
17	POLR2A	chr12:57109462-57111036	GM12891	blood:	n/a	n/a
18	POLR2A	chr12:57109485-57110016	GM12878	blood:	n/a	n/a
19	POLR2A	chr12:57109230-57111658	K562	blood:	n/a	n/a
20	POLR2A	chr12:57109871-57110278	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr12:57109283-57116293	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:57109459-57111272	K562	blood:	n/a	n/a
23	POLR2A	chr12:57109278-57110564	MCF-7	breast:	n/a	n/a
24	POLR2A	chr12:57109342-57110329	HepG2	liver:	n/a	n/a
25	POLR2A	chr12:57109555-57110829	GM12878	blood:	n/a	n/a
26	POLR2A	chr12:57109820-57110122	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr12:57109829-57110731	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr12:57109094-57117058	SK-N-MC	brain:	n/a	n/a
29	POLR2A	chr12:57109763-57110607	U87	brain:	n/a	n/a
30	POLR2A	chr12:57109165-57110714	GM12892	blood:	n/a	n/a
31	POLR2A	chr12:57109930-57110618	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr12:57109523-57109965	A549	lung:	n/a	n/a
33	POLR2A	chr12:57109115-57110514	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr12:57109250-57110612	A549	lung:	n/a	n/a
35	POLR2A	chr12:57109769-57110500	U87	brain:	n/a	n/a
36	POLR2A	chr12:57109564-57110655	GM12892	blood:	n/a	n/a
37	POLR2A	chr12:57108026-57111457	HepG2	liver:	n/a	n/a
38	POLR2A	chr12:57109291-57111137	K562	blood:	n/a	n/a
39	POLR2A	chr12:57109506-57110907	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr12:57109356-57117115	GM12878	blood:	n/a	n/a
41	POLR2A	chr12:57109353-57111565	HL-60	blood:	n/a	n/a
42	POLR2A	chr12:57109498-57110080	GM12878	blood:	n/a	n/a
43	POLR2A	chr12:57109501-57110656	H1-hESC	embryonic stem cell:	n/a	n/a
44	HEY1	chr12:57109521-57110035	K562	blood:	n/a	n/a
45	POLR2A	chr12:57109491-57110693	K562	blood:	n/a	n/a
46	POLR2A	chr12:57109111-57113222	GM12892	blood:	n/a	n/a
47	POLR2A	chr12:57109481-57110867	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr12:57108774-57111413	K562	blood:	n/a	n/a
49	POLR2A	chr12:57109422-57111685	K562	blood:	n/a	n/a
50	POLR2A	chr12:57109520-57110076	H1-hESC	embryonic stem cell:	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
ENSG00000076108	Chromatin interaction
ENSG00000110958	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1026565	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10459246	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10747769	0.83[EUR][1000 genomes]
rs10747770	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10783796	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10876916	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10876918	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171951	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11171956	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1131514	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12828563	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1466382	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1563897	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1975875	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1979325	0.93[ASN][1000 genomes]
rs2035081	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2035082	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2290893	0.83[EUR][1000 genomes]
rs2290894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2926741	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2926743	0.93[ASN][1000 genomes]
rs2926748	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2958127	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2958130	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2958132	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2958134	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2958148	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2958149	0.93[ASN][1000 genomes]
rs2958155	0.81[EUR][1000 genomes]
rs3214051	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4759256	0.86[ASN][1000 genomes]
rs4788	0.92[ASN][1000 genomes]
rs4902	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7137749	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7295862	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7313074	0.86[ASN][1000 genomes]
rs7966391	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7967600	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7978685	0.92[ASN][1000 genomes]
rs7980317	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7980835	0.83[EUR][1000 genomes]
rs898609	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs898611	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9989034	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	esv3378333	chr12:57109685-57113883	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	esv3367526	chr12:57109835-57113733	Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57104000-57114600	Weak transcription	Fetal Brain Male	brain
2	chr12:57104600-57110200	Strong transcription	Fetal Stomach	stomach
3	chr12:57104600-57112600	Strong transcription	Fetal Intestine Large	intestine
4	chr12:57104600-57115000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:57104800-57110000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:57104800-57110000	Strong transcription	Brain Germinal Matrix	brain
7	chr12:57104800-57110000	Strong transcription	Stomach Smooth Muscle	stomach
8	chr12:57104800-57110000	Strong transcription	A549	lung
9	chr12:57104800-57110200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:57104800-57110200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr12:57104800-57110200	Strong transcription	Placenta	Placenta
12	chr12:57104800-57110400	Strong transcription	Primary B cells from peripheral blood	blood
13	chr12:57104800-57110600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr12:57104800-57110600	Strong transcription	Osteobl	bone
15	chr12:57104800-57111000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:57104800-57111200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:57104800-57111200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:57104800-57111200	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:57104800-57111200	Strong transcription	HSMM	muscle
20	chr12:57104800-57111400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:57105000-57110000	Strong transcription	Primary B cells from cord blood	blood
22	chr12:57105000-57110200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr12:57105000-57110200	Strong transcription	Dnd41	blood
24	chr12:57105000-57110400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr12:57105000-57110400	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr12:57105000-57110600	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr12:57105000-57110600	Strong transcription	HepG2	liver
28	chr12:57105000-57110600	Strong transcription	NHDF-Ad	bronchial
29	chr12:57105000-57110800	Strong transcription	Duodenum Mucosa	Duodenum
30	chr12:57105000-57111200	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:57105000-57111400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
32	chr12:57105000-57111600	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr12:57105200-57110000	Strong transcription	Rectal Smooth Muscle	rectum
34	chr12:57105200-57110400	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr12:57105200-57110400	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr12:57105200-57110400	Strong transcription	HSMMtube	muscle
37	chr12:57105200-57110600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr12:57105200-57111200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr12:57105200-57112200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:57105800-57112200	Weak transcription	Fetal Heart	heart
41	chr12:57106000-57110200	Strong transcription	Primary hematopoietic stem cells	blood
42	chr12:57106000-57110600	Strong transcription	Brain Anterior Caudate	brain
43	chr12:57106000-57111000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
44	chr12:57106200-57110000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr12:57106200-57110200	Strong transcription	Primary T cells from cord blood	blood
46	chr12:57106200-57110200	Strong transcription	Fetal Brain Female	brain
47	chr12:57106200-57110200	Strong transcription	Fetal Lung	lung
48	chr12:57106200-57110200	Strong transcription	K562	blood
49	chr12:57106200-57110400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
50	chr12:57106400-57110200	Strong transcription	H9 Cell Line	embryonic stem cell

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