Variant report

Variant	rs772700
Chromosome Location	chr12:56325419-56325420
allele	C/T
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	chr12:56324592-56325967	Raji	blood:	n/a	n/a
2	POLR2A	chr12:56325274-56325513	GM12878	blood:	n/a	n/a
3	CTCF	chr12:56325280-56325430	AG09319	gingival:	n/a	n/a
4	PML	chr12:56324487-56325664	GM12878	blood:	n/a	n/a
5	CTCF	chr12:56324267-56325940	SK-N-SH	brain:	n/a	chr12:56324677-56324685 chr12:56325122-56325130 chr12:56324672-56324690 chr12:56324674-56324695
6	TAL1	chr12:56325370-56325677	K562	blood:	n/a	n/a
7	POLR2A	chr12:56325367-56326819	IMR90	lung:	n/a	n/a
8	POLR2A	chr12:56324680-56325458	GM12892	blood:	n/a	n/a
9	POLR2A	chr12:56325376-56326057	SK-N-SH	brain:	n/a	n/a
10	MAX	chr12:56324555-56326232	ECC-1	luminal epithelium:	n/a	n/a
11	RAD21	chr12:56324368-56326036	SK-N-SH	brain:	n/a	chr12:56324675-56324682 chr12:56325104-56325116 chr12:56324673-56324692 chr12:56324677-56324686
12	MAX	chr12:56325388-56325975	A549	lung:	n/a	n/a
13	ZBTB7A	chr12:56324564-56326489	ECC-1	luminal epithelium:	n/a	n/a
14	STAT5A	chr12:56324979-56325449	GM12878	blood:	n/a	n/a
15	MAZ	chr12:56324459-56326683	IMR90	lung:	n/a	n/a
16	ZBTB7A	chr12:56324803-56326506	ECC-1	luminal epithelium:	n/a	n/a
17	CTCF	chr12:56325320-56325470	AG10803	skin:	n/a	n/a
18	E2F6	chr12:56325254-56325814	H1-hESC	embryonic stem cell:	n/a	chr12:56325312-56325324 chr12:56325588-56325597 chr12:56325590-56325602 chr12:56325770-56325779 chr12:56325582-56325592
19	MAX	chr12:56324438-56326096	A549	lung:	n/a	n/a
20	POLR2A	chr12:56324453-56326067	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr12:56324885-56325492	Hela-S3	cervix:	n/a	n/a
22	RCOR1	chr12:56324541-56325661	K562	blood:	n/a	n/a
23	POLR2A	chr12:56325204-56326134	K562	blood:	n/a	n/a
24	MTA3	chr12:56324328-56325797	GM12878	blood:	n/a	n/a
25	STAT5A	chr12:56324544-56325775	GM12878	blood:	n/a	chr12:56324840-56324849 chr12:56324825-56324848 chr12:56325537-56325549 chr12:56324837-56324851 chr12:56324839-56324848
26	TAF1	chr12:56325221-56326401	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr12:56324418-56325482	HCT-116	colon:	n/a	n/a
28	TCF12	chr12:56325142-56325845	A549	lung:	n/a	n/a
29	POLR2A	chr12:56324741-56326182	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr12:56324501-56325754	GM12891	blood:	n/a	n/a
31	POLR2A	chr12:56325244-56326569	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr12:56324469-56326750	GM12878	blood:	n/a	n/a
33	TCF12	chr12:56324605-56326150	ECC-1	luminal epithelium:	n/a	chr12:56324821-56324828
34	POLR2A	chr12:56324213-56326087	SK-N-MC	brain:	n/a	n/a
35	RUNX3	chr12:56324454-56325478	GM12878	blood:	n/a	n/a
36	E2F6	chr12:56325281-56325893	A549	lung:	n/a	chr12:56325866-56325875 chr12:56325312-56325324 chr12:56325588-56325597 chr12:56325590-56325602 chr12:56325770-56325779 chr12:56325582-56325592

No.	Distal block	Cell Line	Cell type
1	chr12:56324272..56327111-chr12:56385454..56388039,2	MCF-7	breast:
2	chr12:56324645..56327679-chr12:56350066..56352097,3	MCF-7	breast:
3	chr12:56208117..56217611-chr12:56318345..56328982,45	MCF-7	breast:
4	chr12:53341241..53344226-chr12:56323655..56325442,2	MCF-7	breast:
5	chr12:56208546..56216914-chr12:56318326..56328671,24	MCF-7	breast:
6	chr12:56318132..56330507-chr12:56363672..56369798,22	MCF-7	breast:
7	chr12:56319178..56327497-chr12:56356755..56363470,19	MCF-7	breast:
8	chr12:56210239..56212423-chr12:56323809..56326781,2	K562	blood:
9	chr12:56210581..56212423-chr12:56323860..56326781,2	K562	blood:
10	chr12:56325013..56327160-chr12:56358376..56361876,4	MCF-7	breast:
11	chr12:56217992..56226798-chr12:56311494..56331042,68	MCF-7	breast:
12	chr12:56217492..56232243-chr12:56318854..56330686,48	MCF-7	breast:
13	chr12:56318492..56327488-chr12:56364288..56371675,16	MCF-7	breast:
14	chr12:56323623..56326295-chr12:56400061..56402642,2	MCF-7	breast:
15	chr12:56136172..56138342-chr12:56323730..56326497,2	K562	blood:
16	chr12:56324205..56326557-chr12:56345511..56347767,3	MCF-7	breast:
17	chr12:56324707..56325597-chr12:56434977..56435647,2	MCF-7	breast:
18	chr12:56320184..56328034-chr12:56431937..56442233,20	MCF-7	breast:
19	chr12:56217816..56225905-chr12:56319649..56327312,13	K562	blood:
20	chr12:56320862..56327055-chr12:56370927..56377943,9	MCF-7	breast:
21	chr12:56324994..56327276-chr12:56346740..56350037,3	MCF-7	breast:
22	chr12:56319350..56329795-chr12:56348492..56353182,19	MCF-7	breast:

Variant related genes	Relation type
WIBG	TF binding region
DGKA	TF binding region
ENSG00000255990	Chromatin interaction
ENSG00000237493	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000170421	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000258554	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000257390	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000111057	Chromatin interaction
ENSG00000205323	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10128982	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1052206	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10747760	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10783774	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783775	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10876862	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1136082	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12298127	0.86[ASW][hapmap];0.94[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs1384604	1.00[LWK][hapmap]
rs1681070	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1701698	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1701699	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2101718	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4414258	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61956428	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6581087	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs705711	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs705715	0.86[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7135133	0.80[EUR][1000 genomes]
rs7297871	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7302957	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7308505	0.86[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312870	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs772462	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs772468	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs772473	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs772475	0.86[ASW][hapmap];0.83[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs772704	0.87[CEU][hapmap]
rs9739192	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9739196	0.87[EUR][1000 genomes];0.83[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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs772700	GLS2	cis	cerebellum	SCAN
rs772700	LARP4	cis	parietal	SCAN
rs772700	SDR9C7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56319800-56326600	Active TSS	Thymus	Thymus
2	chr12:56321200-56327600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:56321600-56327000	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr12:56321800-56327200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr12:56324000-56326600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
6	chr12:56324000-56326600	Active TSS	Primary T killer memory cells from peripheral blood	blood
7	chr12:56324000-56327000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:56324200-56326400	Active TSS	Primary T cells from cord blood	blood
9	chr12:56324200-56327400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:56324400-56325600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:56324400-56325600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:56324400-56325600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:56324400-56325600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
14	chr12:56324400-56325600	Flanking Active TSS	HMEC	breast
15	chr12:56324400-56326000	Enhancers	Fetal Heart	heart
16	chr12:56324400-56327000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:56324600-56325600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:56324600-56325600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr12:56324600-56325600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
20	chr12:56324600-56325600	Flanking Active TSS	Right Ventricle	heart
21	chr12:56324600-56325600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr12:56324600-56325800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:56324600-56326400	Active TSS	Fetal Thymus	thymus
24	chr12:56324800-56325600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr12:56324800-56325600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr12:56324800-56325600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:56324800-56325600	Flanking Active TSS	Primary B cells from peripheral blood	blood
28	chr12:56324800-56325600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:56324800-56325600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:56324800-56325600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr12:56324800-56325600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:56324800-56325600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:56324800-56325600	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr12:56324800-56325600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
35	chr12:56324800-56325600	Flanking Active TSS	Colon Smooth Muscle	Colon
36	chr12:56324800-56325600	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr12:56324800-56325600	Flanking Active TSS	Placenta Amnion	Placenta Amnion
38	chr12:56324800-56325600	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr12:56324800-56325600	Flanking Active TSS	A549	lung
40	chr12:56324800-56325600	Flanking Active TSS	Hela-S3	cervix
41	chr12:56324800-56325600	Flanking Active TSS	HUVEC	blood vessel
42	chr12:56324800-56325600	Flanking Active TSS	K562	blood
43	chr12:56324800-56325600	Flanking Active TSS	NHLF	lung
44	chr12:56324800-56325800	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr12:56324800-56326400	Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr12:56325000-56325600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
47	chr12:56325000-56325600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr12:56325000-56325600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
49	chr12:56325000-56325600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
50	chr12:56325000-56325600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood

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