Variant report

Variant	rs786429
Chromosome Location	chr12:124087394-124087395
allele	A/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	ZNF263	chr12:124086212-124087425	HEK293-T-REx	kidney:	n/a	n/a
2	POLR2A	chr12:124085974-124087791	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:124087178-124087730	HepG2	liver:	n/a	n/a
4	CEBPB	chr12:124086157-124087568	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr12:124087346-124087500	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr12:124085971-124087901	PFSK-1	brain:	n/a	n/a
7	MXI1	chr12:124086047-124087452	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:124087329-124087743	GM12892	blood:	n/a	n/a
9	POLR2A	chr12:124087174-124087661	K562	blood:	n/a	n/a
10	MYC	chr12:124086096-124087513	NB4	blood:	n/a	chr12:124086817-124086826
11	POLR2A	chr12:124085718-124087673	K562	blood:	n/a	n/a
12	POLR2A	chr12:124085907-124087732	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:124086010-124087877	GM12878	blood:	n/a	n/a
14	MXI1	chr12:124085895-124087731	SK-N-SH	brain:	n/a	n/a
15	STAT3	chr12:124087380-124087420	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr12:124085887-124087957	SK-N-MC	brain:	n/a	n/a
17	POLR2A	chr12:124085985-124087604	GM12891	blood:	n/a	n/a
18	PML	chr12:124085886-124087560	GM12878	blood:	n/a	n/a
19	TFAP2C	chr12:124086345-124087683	Hela-S3	cervix:	n/a	chr12:124086892-124086907
20	HCFC1	chr12:124085899-124087854	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr12:124085890-124087726	GM12892	blood:	n/a	n/a
22	POLR2A	chr12:124085948-124087732	K562	blood:	n/a	n/a
23	POLR2A	chr12:124086117-124087409	NB4	blood:	n/a	n/a
24	TCF12	chr12:124085982-124087444	A549	lung:	n/a	chr12:124086938-124086948
25	POLR2A	chr12:124086012-124087416	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr12:124085969-124087482	Raji	blood:	n/a	n/a
27	SIN3AK20	chr12:124085890-124087803	MCF-7	breast:	n/a	n/a
28	MYC	chr12:124086094-124087428	K562	blood:	n/a	chr12:124086817-124086826
29	ESRRA	chr12:124085992-124088010	GM12878	blood:	n/a	chr12:124087194-124087210
30	MTA3	chr12:124085903-124087890	GM12878	blood:	n/a	n/a
31	HA-E2F1	chr12:124086014-124087555	MCF-7	breast:	n/a	chr12:124086418-124086426 chr12:124086415-124086426 chr12:124086419-124086426 chr12:124086417-124086427 chr12:124086499-124086508 chr12:124086416-124086427 chr12:124086418-124086426
32	CEBPB	chr12:124087260-124087537	A549	lung:	n/a	n/a
33	POLR2A	chr12:124086056-124087526	GM19099	blood:	n/a	n/a
34	CEBPB	chr12:124087240-124087492	HepG2	liver:	n/a	n/a
35	RCOR1	chr12:124085990-124087789	K562	blood:	n/a	n/a
36	NR2F2	chr12:124085830-124087442	K562	blood:	n/a	n/a
37	SIN3A	chr12:124086093-124087582	H1-hESC	embryonic stem cell:	n/a	chr12:124086983-124086994 chr12:124086609-124086618
38	MXI1	chr12:124085827-124087656	IMR90	lung:	n/a	n/a
39	POLR2A	chr12:124086128-124087588	GM12878	blood:	n/a	n/a
40	POLR2A	chr12:124085992-124087829	HepG2	liver:	n/a	n/a
41	RCOR1	chr12:124087317-124087419	Hela-S3	cervix:	n/a	n/a
42	MAX	chr12:124086214-124087433	Hela-S3	cervix:	n/a	chr12:124086817-124086826
43	POLR2A	chr12:124085978-124087453	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr12:124085710-124087596	HepG2	liver:	n/a	n/a
45	WRNIP1	chr12:124086195-124087832	GM12878	blood:	n/a	n/a
46	MAZ	chr12:124087147-124087413	GM12878	blood:	n/a	n/a
47	REST	chr12:124085966-124087622	H1-neurons	neurons:	n/a	chr12:124086966-124086979 chr12:124086498-124086511 chr12:124086334-124086347 chr12:124086459-124086469
48	MYC	chr12:124086017-124087551	K562	blood:	n/a	chr12:124086817-124086826
49	POLR2A	chr12:124086005-124087646	PBDE	blood:	n/a	n/a
50	JUN	chr12:124086010-124087994	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:123872223..123875553-chr12:124085591..124088201,3	MCF-7	breast:
2	chr12:123942486..123944135-chr12:124085124..124087552,2	MCF-7	breast:
3	chr12:123866977..123869044-chr12:124085781..124087608,2	MCF-7	breast:
4	chr12:124067363..124072745-chr12:124084857..124088217,7	K562	blood:
5	chr12:124084988..124092992-chr12:124114351..124121638,14	K562	blood:
6	chr12:124084914..124087862-chr12:124122413..124125179,2	K562	blood:
7	chr12:124087290..124089167-chr12:124099421..124102129,2	MCF-7	breast:
8	chr12:123716171..123718231-chr12:124086645..124088616,2	K562	blood:
9	chr12:123941486..123944276-chr12:124085171..124087519,2	K562	blood:
10	chr12:124085831..124093816-chr12:124094373..124101211,18	MCF-7	breast:
11	chr12:123872056..123874942-chr12:124085224..124088307,3	MCF-7	breast:
12	chr12:123866701..123869300-chr12:124085669..124087764,2	K562	blood:
13	chr12:123755058..123757440-chr12:124084744..124087456,3	K562	blood:
14	chr12:124085496..124088026-chr12:124116630..124119648,4	MCF-7	breast:
15	chr12:124067302..124072457-chr12:124084684..124088760,8	K562	blood:
16	chr12:124086555..124088221-chr12:124100026..124101762,2	K562	blood:
17	chr12:124085449..124088387-chr12:124115552..124120028,6	MCF-7	breast:
18	chr12:124086664..124088557-chr12:124117448..124120033,4	K562	blood:
19	chr12:123847169..123849970-chr12:124085128..124088523,3	K562	blood:
20	chr12:123867386..123869300-chr12:124085669..124087822,2	K562	blood:

Variant related genes	Relation type
DDX55	TF binding region
ENSG00000139697	Chromatin interaction
ENSG00000206897	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000111361	Chromatin interaction
ENSG00000247373	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000184209	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11057298	0.90[CEU][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11057302	1.00[CEU][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057306	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11610013	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615043	0.81[EUR][1000 genomes]
rs11834369	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837236	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12099981	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12099986	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877365	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2340691	1.00[CEU][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3209852	0.81[ASN][1000 genomes]
rs34099549	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748268	0.90[CEU][hapmap]
rs4930715	0.96[EUR][1000 genomes]
rs61678733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488879	0.87[CEU][hapmap]
rs6488881	1.00[CEU][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6488882	0.85[YRI][hapmap]
rs7136101	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7301377	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303554	1.00[CEU][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316613	0.94[EUR][1000 genomes]
rs73414262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs786428	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786431	0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786433	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786435	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786437	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786439	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786450	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786455	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs7954782	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7958153	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960812	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7965292	0.82[YRI][hapmap]
rs7965466	0.84[EUR][1000 genomes]
rs7968040	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970545	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971779	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973689	0.81[YRI][hapmap]
rs884892	0.90[CEU][hapmap]
rs952360	1.00[CEU][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9697379	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS 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 miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	nsv1042181	chr12:124037400-124152950	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs786429	RP11-486O12.2	cis	Artery Aorta	GTEx
rs786429	DDX55	cis	lung	GTEx
rs786429	RP11-486O12.2	cis	Muscle Skeletal	GTEx
rs786429	DDX55	cis	Brain Pons	GTEx
rs786429	DDX55	cis	Esophagus Muscularis	GTEx
rs786429	DDX55	cis	Thyroid	GTEx
rs786429	RP11-486O12.2	cis	Thyroid	GTEx
rs786429	RP11-486O12.2	cis	Esophagus Mucosa	GTEx
rs786429	RP11-486O12.2	cis	Heart Left Ventricle	GTEx
rs786429	RP11-486O12.2	cis	Nerve Tibial	GTEx
rs786429	RP11-486O12.2	cis	Esophagus Muscularis	GTEx
rs786429	RP11-486O12.2	cis	Adipose Subcutaneous	GTEx
rs786429	DDX55	cis	Frontal Cortex	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124085400-124087400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:124085400-124087800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:124085600-124087400	Active TSS	Muscle Satellite Cultured Cells	--
4	chr12:124085600-124087400	Active TSS	HSMM	muscle
5	chr12:124085600-124087400	Active TSS	NHLF	lung
6	chr12:124085600-124087600	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr12:124085600-124087600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:124085600-124087600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:124085600-124087800	Active TSS	Fetal Kidney	kidney
10	chr12:124085600-124088000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:124085600-124088000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:124085600-124088000	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr12:124085600-124088000	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr12:124085600-124088000	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr12:124085600-124088400	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr12:124085600-124088400	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr12:124085800-124087400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:124085800-124087400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:124085800-124087400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:124085800-124087400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:124085800-124087400	Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr12:124085800-124087400	Active TSS	Colon Smooth Muscle	Colon
23	chr12:124085800-124087400	Active TSS	Fetal Lung	lung
24	chr12:124085800-124087400	Active TSS	Left Ventricle	heart
25	chr12:124085800-124087400	Active TSS	Pancreas	Pancrea
26	chr12:124085800-124087400	Active TSS	HSMMtube	muscle
27	chr12:124085800-124087400	Active TSS	K562	blood
28	chr12:124085800-124087400	Active TSS	NHEK	skin
29	chr12:124085800-124087400	Active TSS	Osteobl	bone
30	chr12:124085800-124087600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:124085800-124087600	Active TSS	Esophagus	oesophagus
32	chr12:124085800-124087600	Active TSS	Right Atrium	heart
33	chr12:124085800-124088000	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr12:124085800-124088000	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr12:124085800-124088000	Active TSS	A549	lung
36	chr12:124085800-124088400	Active TSS	GM12878-XiMat	blood
37	chr12:124086000-124087400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr12:124086000-124087400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
39	chr12:124086000-124087400	Active TSS	Gastric	stomach
40	chr12:124086000-124087400	Active TSS	Ovary	ovary
41	chr12:124086000-124087400	Active TSS	Placenta Amnion	Placenta Amnion
42	chr12:124086000-124087400	Active TSS	Small Intestine	intestine
43	chr12:124086000-124087400	Active TSS	NH-A	brain
44	chr12:124086000-124087600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr12:124086000-124087600	Active TSS	H1 Cell Line	embryonic stem cell
46	chr12:124086000-124087600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr12:124086000-124087600	Active TSS	Fetal Intestine Large	intestine
48	chr12:124086000-124087800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr12:124086000-124088000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr12:124086000-124088000	Active TSS	H9 Cell Line	embryonic stem cell

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