Variant report

Variant	rs772473
Chromosome Location	chr12:56322181-56322182
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:89)
CpG islands
(count:0)
Chromatin interactive
region (count:39)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:89 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr12:56321138-56322208	MCF-7	breast:	n/a	chr12:56321697-56321712
2	HCFC1	chr12:56319936-56322295	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr12:56320471-56322278	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:56321261-56322218	H1-hESC	embryonic stem cell:	n/a	n/a
5	MYC	chr12:56320447-56322190	K562	blood:	n/a	n/a
6	POLR2A	chr12:56320505-56322248	Hela-S3	cervix:	n/a	n/a
7	FOXM1	chr12:56320230-56322195	GM12878	blood:	n/a	n/a
8	ELF1	chr12:56320403-56322217	MCF-7	breast:	n/a	chr12:56320909-56320920 chr12:56321484-56321496
9	YY1	chr12:56320384-56322351	H1-hESC	embryonic stem cell:	n/a	chr12:56321484-56321498 chr12:56320885-56320897 chr12:56320747-56320756 chr12:56321466-56321477
10	MAZ	chr12:56320007-56322204	IMR90	lung:	n/a	n/a
11	POLR2A	chr12:56321191-56322203	GM12891	blood:	n/a	n/a
12	POLR2A	chr12:56320076-56322293	GM12878	blood:	n/a	n/a
13	REST	chr12:56320539-56322221	HL-60	blood:	n/a	chr12:56320739-56320752
14	POLR2A	chr12:56320494-56322234	GM12892	blood:	n/a	n/a
15	MAX	chr12:56320479-56322232	MCF-7	breast:	n/a	n/a
16	TCF12	chr12:56319994-56322254	A549	lung:	n/a	n/a
17	ATF2	chr12:56321722-56322259	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr12:56320424-56322425	GM12878	blood:	n/a	n/a
19	MAX	chr12:56319957-56322223	A549	lung:	n/a	n/a
20	POLR2A	chr12:56320421-56322238	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr12:56320188-56322185	K562	blood:	n/a	n/a
22	HDAC2	chr12:56320472-56322186	MCF-7	breast:	n/a	chr12:56320501-56320515 chr12:56321257-56321271 chr12:56321262-56321276
23	POLR2A	chr12:56320374-56322255	HL-60	blood:	n/a	n/a
24	TCF12	chr12:56320257-56322194	ECC-1	luminal epithelium:	n/a	n/a
25	MAX	chr12:56320210-56322183	ECC-1	luminal epithelium:	n/a	n/a
26	MAX	chr12:56320438-56322247	HepG2	liver:	n/a	n/a
27	YY1	chr12:56321997-56322360	K562	blood:	n/a	n/a
28	POLR2A	chr12:56320415-56322223	K562	blood:	n/a	n/a
29	YY1	chr12:56320409-56322696	GM12878	blood:	n/a	chr12:56321484-56321498 chr12:56320885-56320897 chr12:56320747-56320756 chr12:56321466-56321477
30	POLR2A	chr12:56320427-56322272	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr12:56320516-56322278	MCF-7	breast:	n/a	n/a
32	PML	chr12:56320483-56322234	K562	blood:	n/a	chr12:56321973-56321981
33	FOXM1	chr12:56320152-56322293	GM12878	blood:	n/a	n/a
34	MAX	chr12:56320534-56322204	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr12:56319976-56322359	SK-N-MC	brain:	n/a	n/a
36	YY1	chr12:56322067-56322366	K562	blood:	n/a	n/a
37	CBX3	chr12:56321261-56322264	K562	blood:	n/a	n/a
38	POLR2A	chr12:56320537-56322222	Hela-S3	cervix:	n/a	n/a
39	YY1	chr12:56320409-56322723	GM12892	blood:	n/a	chr12:56321484-56321498 chr12:56320885-56320897 chr12:56320747-56320756 chr12:56321466-56321477
40	RUNX3	chr12:56320311-56322244	GM12878	blood:	n/a	chr12:56320898-56320913
41	CTCF	chr12:56322040-56322190	HBMEC	blood vessel:	n/a	n/a
42	PML	chr12:56319991-56322368	GM12878	blood:	n/a	chr12:56321973-56321981
43	POLR2A	chr12:56320384-56322277	K562	blood:	n/a	n/a
44	POLR2A	chr12:56320245-56322195	K562	blood:	n/a	n/a
45	BCLAF1	chr12:56321187-56322187	GM12878	blood:	n/a	chr12:56321882-56321891
46	TCF12	chr12:56320324-56322262	ECC-1	luminal epithelium:	n/a	n/a
47	SMARCB1	chr12:56320610-56322224	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr12:56320429-56322267	GM12892	blood:	n/a	n/a
49	STAT5A	chr12:56321701-56322240	GM12878	blood:	n/a	n/a
50	POLR2A	chr12:56320447-56322462	HepG2	liver:	n/a	n/a

No data

(count:39 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56320958..56322490-chr12:56473085..56475455,2	MCF-7	breast:
2	chr12:56319938..56322898-chr12:56413808..56415647,2	MCF-7	breast:
3	chr12:56320141..56322602-chr12:56350018..56351864,3	MCF-7	breast:
4	chr12:56208117..56217611-chr12:56318345..56328982,45	MCF-7	breast:
5	chr12:56235299..56237964-chr12:56318777..56323177,4	MCF-7	breast:
6	chr12:56320848..56323516-chr12:56414384..56416696,2	K562	blood:
7	chr12:56121779..56124068-chr12:56319367..56323030,5	K562	blood:
8	chr12:56208546..56216914-chr12:56318326..56328671,24	MCF-7	breast:
9	chr12:56318132..56330507-chr12:56363672..56369798,22	MCF-7	breast:
10	chr12:56319178..56327497-chr12:56356755..56363470,19	MCF-7	breast:
11	chr12:56134894..56138354-chr12:56318411..56324580,8	MCF-7	breast:
12	chr12:56319711..56323865-chr12:56387409..56394085,7	MCF-7	breast:
13	chr12:56121796..56124636-chr12:56320580..56323901,5	MCF-7	breast:
14	chr12:56217992..56226798-chr12:56311494..56331042,68	MCF-7	breast:
15	chr12:56210386..56214682-chr12:56319005..56323153,8	K562	blood:
16	chr12:56217492..56232243-chr12:56318854..56330686,48	MCF-7	breast:
17	chr12:56318939..56322802-chr12:56399424..56402892,5	MCF-7	breast:
18	chr12:56321404..56322299-chr9:4679520..4680103,2	NB4	blood:
19	chr12:56318993..56322413-chr12:56389425..56391488,3	K562	blood:
20	chr12:56318492..56327488-chr12:56364288..56371675,16	MCF-7	breast:
21	chr12:56320034..56323218-chr12:56434982..56437337,4	K562	blood:
22	chr12:56318129..56322590-chr12:56359033..56362321,5	K562	blood:
23	chr12:56319082..56322613-chr12:56358459..56362927,5	MCF-7	breast:
24	chr12:56120587..56125243-chr12:56320195..56323478,6	MCF-7	breast:
25	chr12:56122193..56124805-chr12:56319367..56323067,7	K562	blood:
26	chr12:56319021..56322273-chr12:56510153..56512208,3	K562	blood:
27	chr12:56219783..56227072-chr12:56318292..56323886,14	K562	blood:
28	chr12:56320184..56328034-chr12:56431937..56442233,20	MCF-7	breast:
29	chr12:56318513..56323358-chr12:56346151..56349389,6	MCF-7	breast:
30	chr12:56217816..56225905-chr12:56319649..56327312,13	K562	blood:
31	chr12:56320906..56323810-chr12:56434413..56437173,4	MCF-7	breast:
32	chr12:56320942..56323353-chr12:56346248..56347788,2	MCF-7	breast:
33	chr12:56320862..56327055-chr12:56370927..56377943,9	MCF-7	breast:
34	chr12:56209786..56211523-chr12:56320983..56323005,2	K562	blood:
35	chr12:56319967..56322287-chr12:56473106..56474816,2	K562	blood:
36	chr12:56320816..56323380-chr12:64797678..64799344,2	MCF-7	breast:
37	chr12:56319307..56323047-chr12:56359033..56361996,7	K562	blood:
38	chr12:56233687..56236115-chr12:56320248..56323583,3	MCF-7	breast:
39	chr12:56319350..56329795-chr12:56348492..56353182,19	MCF-7	breast:

No data

Variant related genes	Relation type
DGKA	TF binding region
WIBG	TF binding region
ENSG00000258056	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000237493	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000123342	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000184575	Chromatin interaction
ENSG00000106993	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000257390	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000258554	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1052206	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10747760	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10783774	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10783775	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876862	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1136082	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12298127	0.83[AMR][1000 genomes]
rs1681070	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1681082	0.83[AMR][1000 genomes]
rs1701698	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1701699	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2101718	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4414258	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61956428	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6581087	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs705711	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs705715	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7297871	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7308505	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7312870	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs772462	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs772468	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs772700	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9739192	0.82[ASN][1000 genomes]
rs9739196	0.82[ASN][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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 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	chr12:56319600-56322200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:56319800-56322200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr12:56319800-56322200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:56319800-56322400	Active TSS	H9 Cell Line	embryonic stem cell
5	chr12:56319800-56322400	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr12:56319800-56322400	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr12:56319800-56322400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:56319800-56322400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:56319800-56326600	Active TSS	Thymus	Thymus
10	chr12:56320000-56322200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:56320000-56322200	Active TSS	A549	lung
12	chr12:56320000-56322400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:56320000-56322400	Active TSS	Fetal Kidney	kidney
14	chr12:56320000-56322600	Active TSS	H1 Cell Line	embryonic stem cell
15	chr12:56320000-56322600	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr12:56320000-56322600	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr12:56320000-56322600	Active TSS	GM12878-XiMat	blood
18	chr12:56320000-56322800	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr12:56320200-56322200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:56320200-56322200	Active TSS	Aorta	Aorta
21	chr12:56320200-56322200	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr12:56320200-56322200	Active TSS	Gastric	stomach
23	chr12:56320200-56322200	Active TSS	Left Ventricle	heart
24	chr12:56320200-56322200	Active TSS	Placenta Amnion	Placenta Amnion
25	chr12:56320200-56322200	Active TSS	NHLF	lung
26	chr12:56320200-56322400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:56320200-56322400	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr12:56320200-56322400	Active TSS	Pancreas	Pancrea
29	chr12:56320200-56322400	Active TSS	NHEK	skin
30	chr12:56320200-56322600	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr12:56320200-56322600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:56320200-56322600	Active TSS	Small Intestine	intestine
33	chr12:56320400-56322200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:56320400-56322200	Active TSS	Right Atrium	heart
35	chr12:56320400-56322200	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr12:56320400-56322400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:56320400-56322400	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr12:56320400-56322800	Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr12:56320600-56322400	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr12:56320600-56322400	Active TSS	Dnd41	blood
41	chr12:56320600-56322600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:56320600-56322800	Active TSS	Primary T cells from cord blood	blood
43	chr12:56320600-56322800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:56320600-56322800	Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr12:56321000-56322200	Bivalent/Poised TSS	HepG2	liver
46	chr12:56321200-56322200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:56321200-56322600	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr12:56321200-56327600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:56321400-56322200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr12:56321600-56322200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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