Variant report

Variant	rs705702
Chromosome Location	chr12:56390636-56390637
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	HEY1	chr12:56390616-56391305	K562	blood:	n/a	n/a
2	TBL1XR1	chr12:56390456-56391138	K562	blood:	n/a	n/a
3	HNF4G	chr12:56390557-56391313	HepG2	liver:	n/a	chr12:56390858-56390873
4	POLR2A	chr12:56390599-56391893	H1-neurons	neurons:	n/a	n/a
5	RUNX3	chr12:56390589-56391232	GM12878	blood:	n/a	n/a
6	CEBPD	chr12:56390621-56391325	HepG2	liver:	n/a	n/a
7	MAZ	chr12:56389997-56391335	K562	blood:	n/a	n/a
8	REST	chr12:56390614-56390853	A549	lung:	n/a	n/a
9	FOXM1	chr12:56390439-56391378	GM12878	blood:	n/a	n/a
10	UBTF	chr12:56390316-56391270	K562	blood:	n/a	n/a
11	POLR2A	chr12:56390630-56391366	A549	lung:	n/a	n/a
12	RFX5	chr12:56389864-56391654	IMR90	lung:	n/a	chr12:56390916-56390931 chr12:56391640-56391648 chr12:56390917-56390931 chr12:56390915-56390929
13	POLR2A	chr12:56390550-56391350	GM12891	blood:	n/a	n/a
14	POLR2A	chr12:56390523-56391380	HCT-116	colon:	n/a	n/a
15	CTCF	chr12:56390580-56390730	HCFaa	heart:	n/a	n/a
16	CTCF	chr12:56390620-56390770	AG09309	skin:	n/a	n/a
17	JUND	chr12:56390624-56391329	A549	lung:	n/a	n/a
18	POLR2A	chr12:56390495-56391492	SK-N-MC	brain:	n/a	n/a
19	SMC3	chr12:56389911-56391115	HepG2	liver:	n/a	chr12:56390079-56390093 chr12:56390944-56390954
20	PML	chr12:56389963-56391482	K562	blood:	n/a	n/a
21	PBX3	chr12:56390537-56391361	SK-N-SH	brain:	n/a	chr12:56390882-56390902 chr12:56390880-56390889
22	FOXA2	chr12:56390453-56390893	HepG2	liver:	n/a	n/a
23	POLR2A	chr12:56390634-56391298	MCF10A-Er-Src	breast:	n/a	n/a
24	FOXA1	chr12:56390465-56390835	HepG2	liver:	n/a	n/a
25	POLR2A	chr12:56390540-56391706	HL-60	blood:	n/a	n/a
26	CTCF	chr12:56390520-56390670	HPF	lung:	n/a	n/a
27	SP1	chr12:56390517-56391242	HepG2	liver:	n/a	chr12:56391055-56391065 chr12:56391055-56391065 chr12:56391055-56391064 chr12:56391055-56391064 chr12:56391054-56391066 chr12:56391054-56391066 chr12:56391151-56391165 chr12:56391056-56391065 chr12:56391055-56391069
28	POLR2A	chr12:56390459-56391861	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr12:56389878-56391377	PANC-1	pancreas:	n/a	n/a
30	REST	chr12:56390292-56391421	A549	lung:	n/a	chr12:56391051-56391064
31	ZMIZ1	chr12:56390482-56391285	K562	blood:	n/a	n/a
32	BCL3	chr12:56390593-56391360	A549	lung:	n/a	chr12:56391177-56391186 chr12:56391172-56391185
33	SP1	chr12:56390618-56391342	H1-hESC	embryonic stem cell:	n/a	chr12:56391055-56391065 chr12:56391055-56391065 chr12:56391055-56391064 chr12:56391055-56391064 chr12:56391054-56391066 chr12:56391054-56391066 chr12:56391151-56391165 chr12:56391056-56391065 chr12:56391055-56391069
34	MAX	chr12:56389983-56391404	A549	lung:	n/a	n/a
35	TCF12	chr12:56390532-56391711	ECC-1	luminal epithelium:	n/a	chr12:56390723-56390733
36	FOXM1	chr12:56390514-56390994	GM12878	blood:	n/a	n/a
37	MXI1	chr12:56390572-56391339	GM12878	blood:	n/a	n/a
38	FOSL2	chr12:56390563-56391369	HepG2	liver:	n/a	n/a
39	NR2F2	chr12:56389858-56391358	K562	blood:	n/a	n/a
40	CEBPB	chr12:56390481-56391479	Hela-S3	cervix:	n/a	n/a
41	MAFK	chr12:56390597-56391494	Hela-S3	cervix:	n/a	n/a
42	SP1	chr12:56390619-56391210	GM12878	blood:	n/a	chr12:56391055-56391065 chr12:56391055-56391065 chr12:56391055-56391064 chr12:56391055-56391064 chr12:56391054-56391066 chr12:56391054-56391066 chr12:56391151-56391165 chr12:56391056-56391065 chr12:56391055-56391069
43	RFX5	chr12:56389866-56391841	SK-N-SH	brain:	n/a	chr12:56390916-56390931 chr12:56391640-56391648 chr12:56390917-56390931 chr12:56390915-56390929
44	POLR2A	chr12:56390105-56391425	U87	brain:	n/a	n/a
45	SP4	chr12:56390611-56391137	H1-hESC	embryonic stem cell:	n/a	chr12:56391052-56391068 chr12:56391054-56391070
46	POLR2A	chr12:56390452-56391780	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr12:56389874-56391450	K562	blood:	n/a	n/a
48	MTA3	chr12:56389972-56391389	GM12878	blood:	n/a	n/a
49	NFIC	chr12:56390364-56391215	HepG2	liver:	n/a	n/a
50	CCNT2	chr12:56390537-56391305	K562	blood:	n/a	chr12:56391056-56391065

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	chr1:182573061..182573800-chr12:56390620..56391251,2	Hela-S3	cervix:
8	chr12:56318993..56322413-chr12:56389425..56391488,3	K562	blood:
9	chr12:56388983..56390811-chr12:56431023..56433319,3	K562	blood:
10	chr12:56388663..56390972-chr12:56509029..56512021,2	K562	blood:
11	chr12:56389364..56393818-chr12:56396293..56409099,19	MCF-7	breast:
12	chr12:56321159..56321674-chr12:56390128..56390926,2	K562	blood:
13	chr12:56221380..56224964-chr12:56389518..56391626,4	MCF-7	breast:
14	chr12:56386715..56395273-chr12:56398367..56404356,15	MCF-7	breast:
15	chr12:56325939..56329017-chr12:56389529..56391723,3	K562	blood:
16	chr12:56389319..56393039-chr12:56433877..56439169,10	K562	blood:
17	chr12:56390533..56392803-chr12:56508864..56512540,5	K562	blood:
18	chr12:56384784..56387430-chr12:56389499..56392081,3	MCF-7	breast:
19	chr12:56386022..56392601-chr12:56434180..56439537,11	MCF-7	breast:
20	chr12:56388556..56391684-chr12:56495441..56499573,3	K562	blood:
21	chr12:56390059..56391056-chr12:56473265..56474184,2	K562	blood:
22	chr12:56389683..56391012-chr12:56434967..56435949,8	K562	blood:
23	chr12:54346604..54348819-chr12:56388930..56391042,2	MCF-7	breast:
24	chr12:56390277..56392434-chr12:56414994..56416679,2	K562	blood:
25	chr12:56121261..56123274-chr12:56389263..56391155,2	K562	blood:
26	chr12:56222339..56223963-chr12:56389750..56392232,2	MCF-7	breast:
27	chr12:56387772..56393921-chr12:56435042..56439277,13	MCF-7	breast:
28	chr12:56390252..56392502-chr12:56472754..56475150,2	MCF-7	breast:
29	chr12:56326218..56328799-chr12:56389598..56392484,2	K562	blood:
30	chr12:56383457..56387356-chr12:56388448..56393059,5	MCF-7	breast:
31	chr12:56366407..56369311-chr12:56387983..56390869,4	K562	blood:
32	chr12:56209991..56213836-chr12:56388557..56392258,6	MCF-7	breast:
33	chr12:56135587..56138255-chr12:56389747..56392284,4	K562	blood:
34	chr12:56135587..56137703-chr12:56389429..56392012,4	K562	blood:
35	chr12:56387978..56391684-chr12:56496583..56499573,3	K562	blood:
36	chr12:56319711..56323865-chr12:56387409..56394085,7	MCF-7	breast:
37	chr12:56388289..56393996-chr12:56394860..56404076,14	K562	blood:
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:

Variant related genes	Relation type
SUOX	TF binding region
ENSG00000139641	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000258056	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000255990	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000123407	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000143333	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000258554	Chromatin interaction
ENSG00000135482	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 26 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1081975	0.86[ASN][1000 genomes]
rs10876864	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs1131017	0.82[JPT][hapmap]
rs1689510	0.85[EUR][1000 genomes]
rs1701704	0.91[CEU][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs1873914	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];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]
rs2069408	0.89[CHB][hapmap];0.82[YRI][hapmap]
rs2069415	1.00[YRI][hapmap]
rs2456973	0.91[CEU][hapmap];0.82[JPT][hapmap];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	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs705699	0.95[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs705700	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs705704	0.91[CEU][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs772920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772921	0.91[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs773107	0.95[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs773108	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs773109	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];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	0.95[CHB][hapmap];1.00[JPT][hapmap];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

Variant related diseases (count:1)

Disease	PMID	Source
Polycystic ovary syndrome	22885925	GWAS catalog

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs705702	CCDC4	trans	multi-tissue	Pritchard
rs705702	LOC441502	trans	multi-tissue	Pritchard
rs705702	SUOX	cis	multi-tissue	Pritchard
rs705702	LOC644934	trans	multi-tissue	Pritchard
rs705702	RPS26	cis	multi-tissue	Pritchard
rs705702	SUOX	cis	lung	GTEx
rs705702	TAC3	cis	parietal	SCAN
rs705702	RPS26	cis	brain	seeQTL
rs705702	SUOX	cis	Nerve Tibial	GTEx
rs705702	RPS26///RPS26L///LOC644166///LOC644191	cis	uninvolved skin	skin_eQTL
rs705702	LOC441377	trans	multi-tissue	Pritchard
rs705702	MAGEC1	trans	multi-tissue	Pritchard
rs705702	SUOX	cis	parietal	SCAN
rs705702	FLJ20280	trans	multi-tissue	Pritchard
rs705702	RPS26P10	trans	multi-tissue	Pritchard
rs705702	SUOX	cis	Thyroid	GTEx
rs705702	RPS26	trans	brain	seeQTL
rs705702	AC034102.1	cis	Muscle Skeletal	GTEx
rs705702	RPS26///RPS26L///LOC644166///LOC644191	cis	lesional skin	skin_eQTL
rs705702	SUOX	cis	cerebellum	SCAN
rs705702	RAB5B	cis	Muscle Skeletal	GTEx
rs705702	MADCAM1	trans	multi-tissue	Pritchard
rs705702	RPS26	cis	lymphoblastoid	seeQTL
rs705702	DNAJC14	cis	parietal	SCAN
rs705702	CSRNP2	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56389400-56391200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:56389600-56391200	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr12:56389800-56391400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:56389800-56391400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr12:56390000-56390800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:56390000-56390800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr12:56390000-56391200	Active TSS	Brain Angular Gyrus	brain
8	chr12:56390000-56391200	Active TSS	Brain Anterior Caudate	brain
9	chr12:56390000-56391400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:56390000-56391400	Active TSS	Brain Cingulate Gyrus	brain
11	chr12:56390000-56391400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:56390000-56391800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:56390000-56392000	Active TSS	Fetal Kidney	kidney
14	chr12:56390200-56390800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr12:56390200-56390800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr12:56390200-56390800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:56390200-56390800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr12:56390200-56390800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr12:56390200-56390800	Flanking Active TSS	Fetal Lung	lung
20	chr12:56390200-56390800	Flanking Active TSS	NHEK	skin
21	chr12:56390200-56391000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:56390200-56391000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:56390200-56391000	Active TSS	Right Atrium	heart
24	chr12:56390200-56391200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:56390200-56391200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr12:56390200-56391200	Active TSS	Brain Germinal Matrix	brain
27	chr12:56390200-56391200	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr12:56390200-56391200	Active TSS	Colonic Mucosa	Colon
29	chr12:56390200-56391200	Active TSS	Fetal Brain Female	brain
30	chr12:56390200-56391400	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr12:56390200-56391400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:56390200-56391400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:56390200-56391400	Active TSS	Brain Substantia Nigra	brain
34	chr12:56390200-56391400	Active TSS	Left Ventricle	heart
35	chr12:56390200-56391600	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr12:56390200-56391600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:56390200-56391600	Active TSS	Aorta	Aorta
38	chr12:56390200-56391600	Flanking Active TSS	Fetal Brain Male	brain
39	chr12:56390200-56391600	Active TSS	Pancreas	Pancrea
40	chr12:56390200-56391800	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr12:56390200-56391800	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr12:56390200-56391800	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr12:56390200-56391800	Active TSS	Ovary	ovary
44	chr12:56390200-56391800	Active TSS	NH-A	brain
45	chr12:56390200-56392000	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr12:56390200-56392000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:56390200-56392000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:56390200-56392000	Active TSS	Rectal Smooth Muscle	rectum
49	chr12:56390200-56392200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr12:56390400-56390800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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