Variant report

Variant	rs772922
Chromosome Location	chr12:56403953-56403954
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	MYC	chr12:56403938-56404327	K562	blood:	n/a	chr12:56404165-56404174
2	TEAD4	chr12:56403638-56404373	HepG2	liver:	n/a	n/a
3	RCOR1	chr12:56403817-56404464	K562	blood:	n/a	n/a
4	CEBPB	chr12:56403930-56404398	MCF-7	breast:	n/a	chr12:56404163-56404180 chr12:56404165-56404176
5	CCNT2	chr12:56403919-56404281	K562	blood:	n/a	n/a
6	NR2F2	chr12:56403641-56404413	HepG2	liver:	n/a	n/a
7	NFIC	chr12:56403819-56404305	HepG2	liver:	n/a	n/a
8	TBL1XR1	chr12:56403943-56404288	K562	blood:	n/a	n/a
9	NR2F2	chr12:56403700-56404353	HepG2	liver:	n/a	n/a
10	HDAC2	chr12:56403752-56404235	HepG2	liver:	n/a	chr12:56403859-56403873 chr12:56403860-56403874 chr12:56403788-56403802
11	RCOR1	chr12:56403901-56404281	K562	blood:	n/a	n/a
12	HNF4A	chr12:56403734-56404225	HepG2	liver:	n/a	chr12:56404073-56404085 chr12:56404045-56404057 chr12:56404072-56404087 chr12:56404070-56404088 chr12:56404072-56404085 chr12:56404073-56404086 chr12:56404043-56404058 chr12:56404072-56404087 chr12:56404072-56404085 chr12:56404072-56404086 chr12:56404072-56404085 chr12:56404072-56404086 chr12:56404072-56404087 chr12:56404072-56404087 chr12:56404074-56404086 chr12:56404072-56404087
13	ARID3A	chr12:56403930-56404351	K562	blood:	n/a	n/a
14	RXRA	chr12:56403820-56404244	HepG2	liver:	n/a	chr12:56404069-56404089 chr12:56404072-56404085 chr12:56404024-56404033 chr12:56404072-56404085 chr12:56404072-56404085
15	TEAD4	chr12:56403791-56404071	HepG2	liver:	n/a	n/a
16	CEBPB	chr12:56403912-56404296	K562	blood:	n/a	chr12:56404163-56404180 chr12:56404165-56404176
17	HNF4A	chr12:56403863-56404301	HepG2	liver:	n/a	chr12:56404073-56404085 chr12:56404045-56404057 chr12:56404072-56404087 chr12:56404070-56404088 chr12:56404072-56404085 chr12:56404073-56404086 chr12:56404043-56404058 chr12:56404072-56404087 chr12:56404072-56404085 chr12:56404072-56404086 chr12:56404072-56404085 chr12:56404072-56404086 chr12:56404072-56404087 chr12:56404072-56404087 chr12:56404074-56404086 chr12:56404072-56404087
18	HNF4A	chr12:56403803-56404258	HepG2	liver:	n/a	chr12:56404073-56404085 chr12:56404045-56404057 chr12:56404072-56404087 chr12:56404070-56404088 chr12:56404072-56404085 chr12:56404073-56404086 chr12:56404043-56404058 chr12:56404072-56404087 chr12:56404072-56404085 chr12:56404072-56404086 chr12:56404072-56404085 chr12:56404072-56404086 chr12:56404072-56404087 chr12:56404072-56404087 chr12:56404074-56404086 chr12:56404072-56404087
19	EP300	chr12:56403698-56404377	HepG2	liver:	n/a	chr12:56403858-56403872
20	GATA1	chr12:56402729-56404778	K562	blood:	n/a	chr12:56404260-56404273 chr12:56404389-56404400
21	EP300	chr12:56403724-56404321	HepG2	liver:	n/a	chr12:56403858-56403872
22	CEBPD	chr12:56403917-56404401	K562	blood:	n/a	n/a
23	FOXA1	chr12:56403810-56404257	HepG2	liver:	n/a	n/a
24	NFIC	chr12:56403721-56404411	HepG2	liver:	n/a	n/a
25	TEAD4	chr12:56403815-56404284	K562	blood:	n/a	n/a
26	JUN	chr12:56403813-56404955	K562	blood:	n/a	n/a
27	CEBPB	chr12:56403893-56404371	K562	blood:	n/a	chr12:56404163-56404180 chr12:56404165-56404176
28	FOXA2	chr12:56403762-56404275	HepG2	liver:	n/a	n/a
29	FOXA1	chr12:56403648-56404299	HepG2	liver:	n/a	n/a
30	EP300	chr12:56403859-56404342	K562	blood:	n/a	n/a
31	ARID3A	chr12:56403897-56404318	HepG2	liver:	n/a	n/a
32	MYBL2	chr12:56403692-56404405	HepG2	liver:	n/a	n/a
33	NR2F2	chr12:56403872-56404275	K562	blood:	n/a	n/a
34	TCF7L2	chr12:56403788-56404221	HepG2	liver:	n/a	n/a
35	FOXA1	chr12:56403685-56404252	HepG2	liver:	n/a	n/a
36	REST	chr12:56403906-56404216	HepG2	liver:	n/a	chr12:56403974-56403992
37	HNF4G	chr12:56403841-56404274	HepG2	liver:	n/a	chr12:56404073-56404085 chr12:56404045-56404057 chr12:56404072-56404087 chr12:56404070-56404088 chr12:56404072-56404085 chr12:56404073-56404086 chr12:56404072-56404087 chr12:56404072-56404085 chr12:56404072-56404086 chr12:56404072-56404085 chr12:56404072-56404086 chr12:56404070-56404085 chr12:56404072-56404087 chr12:56404072-56404087 chr12:56404044-56404059 chr12:56404074-56404086 chr12:56404072-56404087
38	PML	chr12:56403872-56404376	K562	blood:	n/a	n/a
39	SP1	chr12:56403717-56404395	HepG2	liver:	n/a	chr12:56403750-56403764 chr12:56403958-56403979
40	FOXA1	chr12:56403660-56404286	HepG2	liver:	n/a	n/a
41	TEAD4	chr12:56403716-56404465	K562	blood:	n/a	n/a
42	MYBL2	chr12:56403637-56404348	HepG2	liver:	n/a	n/a
43	HDAC2	chr12:56403741-56404269	HepG2	liver:	n/a	chr12:56403859-56403873 chr12:56403860-56403874 chr12:56403788-56403802

No.	Distal block	Cell Line	Cell type
1	chr12:56398217..56408038-chr12:56433794..56439966,15	K562	blood:
2	chr12:56399175..56403137-chr12:56403716..56405667,4	MCF-7	breast:
3	chr12:56221600..56223437-chr12:56403520..56406122,2	MCF-7	breast:
4	chr12:56388289..56393996-chr12:56394860..56404076,14	K562	blood:
5	chr12:56389364..56393818-chr12:56396293..56409099,19	MCF-7	breast:
6	chr12:56399898..56405642-chr12:56433175..56438589,7	K562	blood:
7	chr12:56400079..56406275-chr12:56406695..56413732,8	MCF-7	breast:
8	chr12:56386715..56395273-chr12:56398367..56404356,15	MCF-7	breast:

Variant related genes	Relation type
IKZF4	TF binding region
ENSG00000197728	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000139531	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1045435	1.00[ASN][1000 genomes]
rs10783777	1.00[ASN][1000 genomes]
rs10783778	1.00[ASN][1000 genomes]
rs10876867	1.00[ASN][1000 genomes]
rs1091527	1.00[ASN][1000 genomes]
rs11171713	0.88[CEU][hapmap]
rs11550558	0.88[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs11835310	1.00[ASN][1000 genomes]
rs11837075	0.87[ASN][1000 genomes]
rs12099979	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs12810011	0.91[EUR][1000 genomes]
rs12815302	0.86[EUR][1000 genomes]
rs12815387	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs12815488	0.91[EUR][1000 genomes]
rs12818756	0.91[EUR][1000 genomes]
rs12831468	0.91[EUR][1000 genomes]
rs12831884	1.00[CEU][hapmap]
rs1614219	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1626158	1.00[ASN][1000 genomes]
rs1689511	1.00[CEU][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1689517	1.00[ASN][1000 genomes]
rs1689518	1.00[ASN][1000 genomes]
rs1701706	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1702876	0.88[AFR][1000 genomes]
rs17118206	0.88[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs17118208	0.88[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs17118262	0.91[EUR][1000 genomes]
rs2131569	0.98[EUR][1000 genomes]
rs2271192	1.00[CHD][hapmap]
rs2271193	1.00[ASN][1000 genomes]
rs2271195	1.00[ASN][1000 genomes]
rs2277340	1.00[ASN][1000 genomes]
rs2456972	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2640566	1.00[ASN][1000 genomes]
rs2658479	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2661728	1.00[ASN][1000 genomes]
rs2661729	1.00[ASN][1000 genomes]
rs2934152	1.00[ASN][1000 genomes]
rs34228181	0.91[EUR][1000 genomes]
rs34303864	0.91[EUR][1000 genomes]
rs34406511	0.91[EUR][1000 genomes]
rs34485293	0.89[EUR][1000 genomes]
rs34507011	0.96[EUR][1000 genomes]
rs34602183	0.87[EUR][1000 genomes]
rs34650555	0.91[EUR][1000 genomes]
rs34921584	0.91[EUR][1000 genomes]
rs35485002	0.94[EUR][1000 genomes]
rs35961650	0.93[EUR][1000 genomes]
rs4759022	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4759239	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71459334	0.91[EUR][1000 genomes]
rs71459336	0.89[EUR][1000 genomes]
rs71459339	0.91[EUR][1000 genomes]
rs7298818	0.92[EUR][1000 genomes]
rs7300292	1.00[ASN][1000 genomes]
rs7300772	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7304690	1.00[ASN][1000 genomes]
rs7311008	1.00[CHD][hapmap]
rs73338377	1.00[ASN][1000 genomes]
rs73338385	1.00[ASN][1000 genomes]
rs73338396	0.87[ASN][1000 genomes]
rs772919	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs772923	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs773115	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963590	0.87[EUR][1000 genomes]
rs7970035	1.00[ASN][1000 genomes]
rs7977537	0.86[EUR][1000 genomes]
rs9738143	1.00[ASN][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	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
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs772922	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs772922	RPS26	cis	lymphoblastoid	seeQTL
rs772922	RDH5	cis	lymphoblastoid	seeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56402000-56418600	Weak transcription	Gastric	stomach
2	chr12:56402200-56404200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:56402200-56404400	Enhancers	Adipose Nuclei	Adipose
4	chr12:56402200-56404600	Enhancers	Fetal Intestine Small	intestine
5	chr12:56402200-56404800	Enhancers	K562	blood
6	chr12:56402200-56405200	Weak transcription	Aorta	Aorta
7	chr12:56402200-56405400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:56402200-56405400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr12:56402200-56405400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:56402200-56405400	Weak transcription	HSMM	muscle
11	chr12:56402200-56407200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr12:56402200-56407400	Weak transcription	Colonic Mucosa	Colon
13	chr12:56402200-56408200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr12:56402200-56409200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:56402200-56411200	Weak transcription	Fetal Muscle Leg	muscle
16	chr12:56402200-56411800	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:56402200-56412600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr12:56402200-56413200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:56402200-56413400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:56402200-56413800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:56402200-56413800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:56402200-56414000	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr12:56402200-56414000	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr12:56402200-56414200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:56402200-56414200	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr12:56402200-56414400	Weak transcription	Primary B cells from cord blood	blood
27	chr12:56402200-56414400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:56402200-56414400	Weak transcription	Brain Angular Gyrus	brain
29	chr12:56402200-56414400	Weak transcription	Brain Substantia Nigra	brain
30	chr12:56402200-56414400	Weak transcription	Left Ventricle	heart
31	chr12:56402200-56414400	Weak transcription	Right Ventricle	heart
32	chr12:56402200-56414400	Weak transcription	Spleen	Spleen
33	chr12:56402200-56414600	Weak transcription	Thymus	Thymus
34	chr12:56402200-56415000	Weak transcription	Lung	lung
35	chr12:56402200-56415200	Weak transcription	NH-A	brain
36	chr12:56402200-56418400	Weak transcription	Pancreas	Pancrea
37	chr12:56402200-56418400	Weak transcription	HSMMtube	muscle
38	chr12:56402200-56434800	Weak transcription	Psoas Muscle	Psoas
39	chr12:56402400-56404200	Weak transcription	Fetal Lung	lung
40	chr12:56402400-56404400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr12:56402400-56404400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr12:56402400-56404400	Enhancers	Fetal Kidney	kidney
43	chr12:56402400-56405200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:56402400-56405200	Weak transcription	Fetal Muscle Trunk	muscle
45	chr12:56402400-56405400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:56402400-56405400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr12:56402400-56405400	Weak transcription	Hela-S3	cervix
48	chr12:56402400-56407400	Weak transcription	Fetal Brain Female	brain
49	chr12:56402400-56407400	Weak transcription	Stomach Mucosa	stomach
50	chr12:56402400-56408000	Weak transcription	Brain Anterior Caudate	brain

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