Variant report

Variant	rs772920
Chromosome Location	chr12:56390364-56390365
allele	C/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	POLR2A	chr12:56390326-56390371	GM12878	blood:	n/a	n/a
2	MAFF	chr12:56390348-56390366	K562	blood:	n/a	n/a
3	MAX	chr12:56390221-56390454	K562	blood:	n/a	n/a
4	MAZ	chr12:56389997-56391335	K562	blood:	n/a	n/a
5	CTCF	chr12:56390286-56390426	GM19240	blood:	n/a	n/a
6	UBTF	chr12:56390316-56391270	K562	blood:	n/a	n/a
7	RFX5	chr12:56389864-56391654	IMR90	lung:	n/a	chr12:56390916-56390931 chr12:56391640-56391648 chr12:56390917-56390931 chr12:56390915-56390929
8	SMC3	chr12:56389911-56391115	HepG2	liver:	n/a	chr12:56390079-56390093 chr12:56390944-56390954
9	PML	chr12:56389963-56391482	K562	blood:	n/a	n/a
10	POLR2A	chr12:56389878-56391377	PANC-1	pancreas:	n/a	n/a
11	REST	chr12:56390292-56391421	A549	lung:	n/a	chr12:56391051-56391064
12	MAX	chr12:56389983-56391404	A549	lung:	n/a	n/a
13	NR2F2	chr12:56389858-56391358	K562	blood:	n/a	n/a
14	RAD21	chr12:56389794-56390524	HCT-116	colon:	n/a	chr12:56390083-56390095 chr12:56390078-56390097
15	RFX5	chr12:56389866-56391841	SK-N-SH	brain:	n/a	chr12:56390916-56390931 chr12:56391640-56391648 chr12:56390917-56390931 chr12:56390915-56390929
16	RAD21	chr12:56389787-56390420	HCT-116	colon:	n/a	chr12:56390083-56390095 chr12:56390078-56390097
17	POLR2A	chr12:56390105-56391425	U87	brain:	n/a	n/a
18	POLR2A	chr12:56389874-56391450	K562	blood:	n/a	n/a
19	MTA3	chr12:56389972-56391389	GM12878	blood:	n/a	n/a
20	NFIC	chr12:56390364-56391215	HepG2	liver:	n/a	n/a
21	CTCF	chr12:56390360-56390510	WI-38	lung:	n/a	n/a
22	RFX5	chr12:56389911-56391486	Hela-S3	cervix:	n/a	chr12:56390916-56390931 chr12:56390917-56390931 chr12:56390915-56390929
23	SIN3AK20	chr12:56389949-56390377	A549	lung:	n/a	n/a
24	RAD21	chr12:56389833-56390374	ECC-1	luminal epithelium:	n/a	chr12:56390083-56390095 chr12:56390078-56390097
25	POLR2A	chr12:56389868-56391375	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr12:56389875-56391712	K562	blood:	n/a	n/a
27	NFATC1	chr12:56390276-56391368	GM12878	blood:	n/a	n/a
28	CTCF	chr12:56390296-56390404	GM12891	blood:	n/a	n/a
29	RAD21	chr12:56389826-56390491	HepG2	liver:	n/a	chr12:56390083-56390095 chr12:56390078-56390097
30	RAD21	chr12:56389883-56390370	MCF-7	breast:	n/a	chr12:56390083-56390095 chr12:56390078-56390097
31	ARID3A	chr12:56389921-56391031	K562	blood:	n/a	n/a
32	POLR2A	chr12:56390018-56391497	U87	brain:	n/a	n/a
33	KAP1	chr12:56390038-56391352	HEK293	kidney:	n/a	n/a
34	TBL1XR1	chr12:56389912-56391194	K562	blood:	n/a	n/a
35	MTA3	chr12:56389953-56391497	GM12878	blood:	n/a	n/a
36	CBX3	chr12:56389921-56391313	K562	blood:	n/a	n/a
37	POLR2A	chr12:56389837-56391392	PFSK-1	brain:	n/a	n/a
38	POLR2A	chr12:56390208-56391586	K562	blood:	n/a	n/a
39	TEAD4	chr12:56389937-56391172	HepG2	liver:	n/a	n/a
40	CTCF	chr12:56389800-56390546	HCT-116	colon:	n/a	chr12:56390077-56390095 chr12:56390079-56390100
41	BCL3	chr12:56389804-56391558	A549	lung:	n/a	chr12:56391177-56391186 chr12:56391172-56391185
42	IRF1	chr12:56389975-56391252	K562	blood:	n/a	chr12:56390475-56390488 chr12:56390472-56390486 chr12:56390985-56390994 chr12:56390475-56390488 chr12:56391052-56391066 chr12:56390476-56390486 chr12:56390476-56390490 chr12:56390762-56390779 chr12:56390475-56390487 chr12:56390475-56390486 chr12:56390475-56390489 chr12:56390959-56390968
43	CTCF	chr12:56390307-56390401	GM19238	blood:	n/a	n/a
44	FOXM1	chr12:56389798-56390400	GM12878	blood:	n/a	n/a
45	RCOR1	chr12:56389949-56391239	K562	blood:	n/a	n/a
46	RCOR1	chr12:56390066-56391037	K562	blood:	n/a	n/a
47	RCOR1	chr12:56389973-56390373	Hela-S3	cervix:	n/a	n/a
48	EP300	chr12:56389888-56391224	K562	blood:	n/a	chr12:56391009-56391022
49	ARID3A	chr12:56389916-56390609	HepG2	liver:	n/a	n/a
50	CTCF	chr12:56389821-56390393	A549	lung:	n/a	chr12:56390077-56390095 chr12:56390079-56390100

No.	Distal block	Cell Line	Cell type
1	chr12:56389589..56390899-chr12:56423167..56424178,10	K562	blood:
2	chr12:56384934..56392097-chr12:56507991..56512680,9	MCF-7	breast:
3	chr12:56365739..56372949-chr12:56384756..56392202,12	MCF-7	breast:
4	chr12:56360624..56364064-chr12:56389013..56391447,3	K562	blood:
5	chr12:56213031..56213738-chr12:56389975..56390706,2	MCF-7	breast:
6	chr12:56365099..56368915-chr12:56389537..56395397,5	K562	blood:
7	chr12:56318993..56322413-chr12:56389425..56391488,3	K562	blood:
8	chr12:56388983..56390811-chr12:56431023..56433319,3	K562	blood:
9	chr12:56388663..56390972-chr12:56509029..56512021,2	K562	blood:
10	chr12:56389364..56393818-chr12:56396293..56409099,19	MCF-7	breast:
11	chr12:56321159..56321674-chr12:56390128..56390926,2	K562	blood:
12	chr12:56221380..56224964-chr12:56389518..56391626,4	MCF-7	breast:
13	chr12:56386715..56395273-chr12:56398367..56404356,15	MCF-7	breast:
14	chr12:56325939..56329017-chr12:56389529..56391723,3	K562	blood:
15	chr12:56389319..56393039-chr12:56433877..56439169,10	K562	blood:
16	chr12:56384784..56387430-chr12:56389499..56392081,3	MCF-7	breast:
17	chr12:56386022..56392601-chr12:56434180..56439537,11	MCF-7	breast:
18	chr12:56388556..56391684-chr12:56495441..56499573,3	K562	blood:
19	chr12:56390059..56391056-chr12:56473265..56474184,2	K562	blood:
20	chr12:56389683..56391012-chr12:56434967..56435949,8	K562	blood:
21	chr12:54346604..54348819-chr12:56388930..56391042,2	MCF-7	breast:
22	chr12:56390277..56392434-chr12:56414994..56416679,2	K562	blood:
23	chr12:56121261..56123274-chr12:56389263..56391155,2	K562	blood:
24	chr12:56222339..56223963-chr12:56389750..56392232,2	MCF-7	breast:
25	chr12:56387772..56393921-chr12:56435042..56439277,13	MCF-7	breast:
26	chr12:56390252..56392502-chr12:56472754..56475150,2	MCF-7	breast:
27	chr12:56326218..56328799-chr12:56389598..56392484,2	K562	blood:
28	chr12:56383457..56387356-chr12:56388448..56393059,5	MCF-7	breast:
29	chr12:56366407..56369311-chr12:56387983..56390869,4	K562	blood:
30	chr12:56209991..56213836-chr12:56388557..56392258,6	MCF-7	breast:
31	chr12:56135587..56138255-chr12:56389747..56392284,4	K562	blood:
32	chr12:56135587..56137703-chr12:56389429..56392012,4	K562	blood:
33	chr12:56387978..56391684-chr12:56496583..56499573,3	K562	blood:
34	chr12:56319711..56323865-chr12:56387409..56394085,7	MCF-7	breast:
35	chr12:56388289..56393996-chr12:56394860..56404076,14	K562	blood:
36	chr12:56389561..56390517-chr12:56434679..56435890,12	MCF-7	breast:
37	chr12:56389662..56390603-chr12:56423076..56424120,8	MCF-7	breast:
38	chr12:56388988..56394527-chr12:56433794..56442585,20	K562	blood:
39	chr12:56389168..56393063-chr12:56410604..56414258,3	K562	blood:
40	chr12:56387786..56391013-chr12:56472110..56474187,3	MCF-7	breast:
41	chr12:56389728..56391330-chr12:56405185..56407283,2	K562	blood:
42	chr12:56349415..56349945-chr12:56389669..56390489,2	MCF-7	breast:

Variant related genes	Relation type
SUOX	TF binding region
ENSG00000135414	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000258056	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000255990	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000258554	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000123407	Chromatin interaction
ENSG00000185664	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1081975	0.86[ASN][1000 genomes]
rs1689510	0.85[EUR][1000 genomes]
rs1701704	0.81[EUR][1000 genomes]
rs1873914	0.93[ASN][1000 genomes]
rs2017445	0.80[EUR][1000 genomes]
rs2048036	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2456973	0.80[EUR][1000 genomes]
rs34415530	0.81[EUR][1000 genomes]
rs61937247	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61937248	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61937249	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61938962	0.81[EUR][1000 genomes]
rs61938963	0.81[EUR][1000 genomes]
rs705698	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs705699	0.86[ASN][1000 genomes]
rs705700	0.90[ASN][1000 genomes]
rs705702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705704	0.80[EUR][1000 genomes]
rs772921	0.84[EUR][1000 genomes]
rs773107	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs773108	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs773109	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs773110	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs773111	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs773112	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs773114	0.88[ASN][1000 genomes]
rs773125	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs772920	RAB5B	cis	Muscle Skeletal	GTEx
rs772920	RPS26	cis	multi-tissue	Pritchard
rs772920	DEFB124	trans	lymphoblastoid	RTeQTL
rs772920	AC034102.1	cis	Muscle Skeletal	GTEx
rs772920	SUOX	cis	Thyroid	GTEx
rs772920	SUOX	cis	Nerve Tibial	GTEx
rs772920	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs772920	SUOX	cis	lung	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56375800-56390600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:56385200-56390600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:56387400-56390400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:56387800-56390400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr12:56388000-56390400	Weak transcription	HMEC	breast
6	chr12:56388000-56390600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:56388000-56390600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:56388200-56390400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:56388200-56390400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:56388200-56390600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:56388200-56390600	Weak transcription	Gastric	stomach
12	chr12:56388200-56390600	Weak transcription	Lung	lung
13	chr12:56388200-56390600	Weak transcription	Spleen	Spleen
14	chr12:56388400-56390400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr12:56388600-56390600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:56388600-56390600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr12:56388800-56390600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:56389000-56390400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr12:56389000-56390600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:56389400-56390400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr12:56389400-56390400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr12:56389400-56390400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr12:56389400-56391200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:56389600-56390400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:56389600-56390400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr12:56389600-56390400	Weak transcription	HSMM	muscle
27	chr12:56389600-56390400	Weak transcription	HSMMtube	muscle
28	chr12:56389600-56391200	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr12:56389800-56390400	Enhancers	HUVEC	blood vessel
30	chr12:56389800-56390600	Enhancers	Primary B cells from peripheral blood	blood
31	chr12:56389800-56390600	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr12:56389800-56390600	Flanking Active TSS	Liver	Liver
33	chr12:56389800-56390600	Enhancers	Fetal Thymus	thymus
34	chr12:56389800-56391400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:56389800-56391400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr12:56390000-56390400	Flanking Active TSS	K562	blood
37	chr12:56390000-56390600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr12:56390000-56390600	Weak transcription	Small Intestine	intestine
39	chr12:56390000-56390800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:56390000-56390800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr12:56390000-56391200	Active TSS	Brain Angular Gyrus	brain
42	chr12:56390000-56391200	Active TSS	Brain Anterior Caudate	brain
43	chr12:56390000-56391400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:56390000-56391400	Active TSS	Brain Cingulate Gyrus	brain
45	chr12:56390000-56391400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:56390000-56391800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:56390000-56392000	Active TSS	Fetal Kidney	kidney
48	chr12:56390200-56390400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr12:56390200-56390400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:56390200-56390400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast

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