Variant report

Variant	rs2230681
Chromosome Location	chr12:122326812-122326813
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	SIN3A	chr12:122326157-122327467	H1-hESC	embryonic stem cell:	n/a	chr12:122326573-122326584
2	ZNF384	chr12:122326215-122327337	K562	blood:	n/a	n/a
3	CTCF	chr12:122326190-122327245	IMR90	lung:	n/a	chr12:122326573-122326586
4	ZMIZ1	chr12:122326153-122327293	K562	blood:	n/a	n/a
5	CREB1	chr12:122326194-122327285	K562	blood:	n/a	n/a
6	EGR1	chr12:122326381-122326840	GM12878	blood:	n/a	chr12:122326507-122326529
7	MYC	chr12:122326168-122327143	K562	blood:	n/a	chr12:122326467-122326476 chr12:122326565-122326572 chr12:122326561-122326576 chr12:122326559-122326574
8	POLR2A	chr12:122326200-122327056	GM12891	blood:	n/a	n/a
9	USF1	chr12:122326048-122327013	A549	lung:	n/a	n/a
10	POLR2A	chr12:122326383-122326931	A549	lung:	n/a	n/a
11	POLR2A	chr12:122326189-122326981	U87	brain:	n/a	n/a
12	MBD4	chr12:122326171-122327118	HepG2	liver:	n/a	n/a
13	MAZ	chr12:122326133-122327304	K562	blood:	n/a	chr12:122326467-122326476 chr12:122326565-122326572 chr12:122326561-122326576 chr12:122326559-122326574
14	RAD21	chr12:122325879-122327331	HCT-116	colon:	n/a	chr12:122327047-122327056
15	IRF1	chr12:122325781-122327382	K562	blood:	n/a	chr12:122326467-122326476 chr12:122326622-122326636 chr12:122326677-122326691
16	TAF1	chr12:122326207-122327174	MCF-7	breast:	n/a	n/a
17	POLR2A	chr12:122326297-122327075	Gliobla	brain:	n/a	n/a
18	ELK1	chr12:122326167-122327185	Hela-S3	cervix:	n/a	n/a
19	CCNT2	chr12:122326139-122327164	K562	blood:	n/a	chr12:122326626-122326635
20	MAX	chr12:122326036-122327447	K562	blood:	n/a	chr12:122326467-122326476 chr12:122326565-122326572 chr12:122326561-122326576 chr12:122326559-122326574
21	TCF3	chr12:122326269-122326876	GM12878	blood:	n/a	n/a
22	CTCF	chr12:122326220-122327250	GM12878	blood:	n/a	chr12:122326573-122326586
23	MYC	chr12:122326314-122326935	MCF-7	breast:	n/a	chr12:122326467-122326476 chr12:122326565-122326572 chr12:122326561-122326576 chr12:122326559-122326574
24	MAFK	chr12:122326177-122327139	Hela-S3	cervix:	n/a	n/a
25	REST	chr12:122326300-122326860	SK-N-SH	brain:	n/a	n/a
26	MYC	chr12:122326306-122327288	MCF10A-Er-Src	breast:	n/a	chr12:122326467-122326476 chr12:122326565-122326572 chr12:122326561-122326576 chr12:122326559-122326574
27	CREB1	chr12:122326331-122326856	A549	lung:	n/a	n/a
28	MAX	chr12:122325932-122327531	A549	lung:	n/a	chr12:122326467-122326476 chr12:122326565-122326572 chr12:122326561-122326576 chr12:122326559-122326574
29	RCOR1	chr12:122326063-122327296	Hela-S3	cervix:	n/a	n/a
30	SMC3	chr12:122326196-122327451	K562	blood:	n/a	n/a
31	KAP1	chr12:122325991-122327112	U2OS	brain:	n/a	n/a
32	EP300	chr12:122326322-122326818	HepG2	liver:	n/a	n/a
33	WRNIP1	chr12:122326153-122327326	GM12878	blood:	n/a	n/a
34	E2F4	chr12:122326340-122326819	GM12878	blood:	n/a	chr12:122326670-122326677
35	EBF1	chr12:122326698-122327144	GM12878	blood:	n/a	chr12:122326948-122326957
36	YY1	chr12:122326143-122327248	GM12878	blood:	n/a	n/a
37	HDAC2	chr12:122326045-122326837	K562	blood:	n/a	chr12:122326646-122326655
38	RAD21	chr12:122326208-122327216	H1-hESC	embryonic stem cell:	n/a	chr12:122327047-122327056
39	NR3C1	chr12:122326256-122327001	A549	lung:	n/a	n/a
40	YY1	chr12:122326294-122327245	K562	blood:	n/a	n/a
41	UBTF	chr12:122326310-122327196	K562	blood:	n/a	n/a
42	BHLHE40	chr12:122326133-122327109	HepG2	liver:	n/a	n/a
43	SIN3AK20	chr12:122326091-122327157	A549	lung:	n/a	n/a
44	TAF7	chr12:122326338-122327196	H1-hESC	embryonic stem cell:	n/a	n/a
45	MYC	chr12:122326157-122327396	K562	blood:	n/a	chr12:122326467-122326476 chr12:122326565-122326572 chr12:122326561-122326576 chr12:122326559-122326574
46	NFIC	chr12:122326099-122327270	GM12878	blood:	n/a	n/a
47	TBP	chr12:122326035-122327270	K562	blood:	n/a	n/a
48	TEAD4	chr12:122325890-122327491	K562	blood:	n/a	n/a
49	CTCF	chr12:122326177-122327209	K562	blood:	n/a	chr12:122326573-122326586
50	POLR2A	chr12:122326140-122327127	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:32345006..32345628-chr12:122326309..122326864,2	Hela-S3	cervix:
2	chr12:122212415..122216174-chr12:122326415..122328726,3	K562	blood:
3	chr12:122231775..122233087-chr12:122326346..122327350,5	MCF-7	breast:
4	chr12:122325656..122327392-chr12:122459155..122461282,2	K562	blood:
5	chr12:122228836..122242951-chr12:122324438..122335797,34	K562	blood:
6	chr12:122213395..122216201-chr12:122325531..122328146,2	MCF-7	breast:
7	chr12:122231812..122233476-chr12:122325996..122327591,21	K562	blood:
8	chr12:122232032..122233517-chr12:122325701..122326925,10	MCF-7	breast:
9	chr12:122228999..122246158-chr12:122324401..122342013,93	MCF-7	breast:
10	chr12:122214229..122218603-chr12:122325636..122328202,4	MCF-7	breast:
11	chr12:122326753..122329169-chr12:122336409..122338553,2	K562	blood:
12	chr12:122232031..122232725-chr12:122326601..122327197,2	MCF-7	breast:
13	chr12:122325518..122327854-chr12:122516363..122518486,3	K562	blood:
14	chr12:122231564..122242843-chr12:122324518..122333366,33	K562	blood:
15	chr1:16840089..16840893-chr12:122326326..122327026,2	Hela-S3	cervix:
16	chr12:122325172..122329151-chr12:122329541..122333817,7	MCF-7	breast:
17	chr12:122213751..122214258-chr12:122326222..122327055,2	MCF-7	breast:
18	chr12:122063686..122066969-chr12:122326410..122329127,3	K562	blood:
19	chr12:122228992..122246947-chr12:122322343..122339116,70	MCF-7	breast:
20	chr12:122326336..122328188-chr12:122688489..122691049,2	MCF-7	breast:
21	chr12:122326249..122328617-chr12:122709300..122711997,3	K562	blood:
22	chr12:122325289..122328252-chr12:122355129..122358130,3	MCF-7	breast:

Variant related genes	Relation type
PSMD9	TF binding region
ENSG00000170759	Chromatin interaction
ENSG00000182500	Chromatin interaction
ENSG00000272849	Chromatin interaction
ENSG00000175727	Chromatin interaction
ENSG00000110987	Chromatin interaction
ENSG00000188735	Chromatin interaction
ENSG00000110801	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000184047	Chromatin interaction
ENSG00000176383	Chromatin interaction
ENSG00000158023	Chromatin interaction
ENSG00000206652	Chromatin interaction
ENSG00000139718	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10770186	0.82[YRI][hapmap]
rs10840626	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10840627	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11043222	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11043226	0.85[AMR][1000 genomes]
rs11502392	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1154510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1154513	0.87[EUR][1000 genomes]
rs1154515	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11614623	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1168674	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1169077	0.82[CEU][hapmap]
rs1169085	0.82[CEU][hapmap]
rs1169093	0.82[CEU][hapmap]
rs1182927	0.82[CEU][hapmap]
rs1185260	1.00[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs1667580	0.88[EUR][1000 genomes]
rs1667583	1.00[CEU][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs1667584	0.87[EUR][1000 genomes]
rs1678951	0.87[EUR][1000 genomes]
rs1678967	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1678969	0.84[CEU][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs1720041	0.82[CEU][hapmap]
rs1720067	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1795963	0.80[CHB][hapmap]
rs1795967	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1947826	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2101017	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2247139	0.88[EUR][1000 genomes]
rs2247291	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2309274	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2596137	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2596144	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2620332	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2620340	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2688412	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2707056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2707075	0.86[ASN][1000 genomes]
rs4760099	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493519	1.00[CEU][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs6486782	0.82[YRI][hapmap]
rs6486794	0.82[CEU][hapmap]
rs693277	0.87[EUR][1000 genomes]
rs7314056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7957207	0.91[CEU][hapmap]
rs7961103	0.91[CEU][hapmap]
rs830122	0.82[CEU][hapmap]
rs830124	1.00[CEU][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap]
rs830126	0.81[EUR][1000 genomes]
rs853758	1.00[CEU][hapmap]
rs895958	1.00[CEU][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs895959	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9668191	0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2230681	CCDC62	cis	parietal	SCAN
rs2230681	RNF10	cis	cerebellum	SCAN
rs2230681	SETD1B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122325800-122327400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:122325800-122327400	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr12:122325800-122327400	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr12:122325800-122327600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:122325800-122328000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:122325800-122328000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:122325800-122328200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:122325800-122328600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:122326000-122327200	Active TSS	H1 Cell Line	embryonic stem cell
10	chr12:122326000-122327200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:122326000-122327200	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr12:122326000-122327200	Active TSS	Stomach Mucosa	stomach
13	chr12:122326000-122327200	Active TSS	Osteobl	bone
14	chr12:122326000-122327400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:122326000-122327400	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr12:122326000-122327400	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr12:122326000-122327400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:122326000-122327400	Active TSS	Fetal Intestine Large	intestine
19	chr12:122326000-122327400	Active TSS	Fetal Muscle Trunk	muscle
20	chr12:122326000-122327400	Active TSS	Fetal Stomach	stomach
21	chr12:122326000-122327400	Active TSS	Psoas Muscle	Psoas
22	chr12:122326000-122327400	Active TSS	NH-A	brain
23	chr12:122326000-122327600	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr12:122326000-122327600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:122326000-122327600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:122326000-122327600	Active TSS	Colonic Mucosa	Colon
27	chr12:122326000-122327600	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr12:122326000-122327600	Active TSS	HSMM	muscle
29	chr12:122326000-122327800	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr12:122326000-122327800	Active TSS	H9 Cell Line	embryonic stem cell
31	chr12:122326000-122327800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:122326000-122327800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:122326000-122327800	Active TSS	NHLF	lung
34	chr12:122326000-122328000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr12:122326200-122327000	Active TSS	Primary hematopoietic stem cells	blood
36	chr12:122326200-122327200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr12:122326200-122327200	Active TSS	Thymus	Thymus
38	chr12:122326200-122327400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:122326200-122327400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:122326200-122327400	Active TSS	Aorta	Aorta
41	chr12:122326200-122327400	Active TSS	Brain Substantia Nigra	brain
42	chr12:122326200-122327400	Active TSS	Esophagus	oesophagus
43	chr12:122326200-122327400	Active TSS	Gastric	stomach
44	chr12:122326200-122327400	Active TSS	Left Ventricle	heart
45	chr12:122326200-122327400	Active TSS	Pancreas	Pancrea
46	chr12:122326200-122327400	Active TSS	Placenta Amnion	Placenta Amnion
47	chr12:122326200-122327400	Active TSS	Right Ventricle	heart
48	chr12:122326200-122327400	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr12:122326200-122327400	Active TSS	Small Intestine	intestine
50	chr12:122326200-122327400	Active TSS	Spleen	Spleen

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