Variant report

Variant	rs786428
Chromosome Location	chr12:124086998-124086999
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	MAX	chr12:124085983-124087355	HCT-116	colon:	n/a	chr12:124086817-124086826
2	POLR2A	chr12:124086159-124087198	HCT-116	colon:	n/a	n/a
3	MXI1	chr12:124086177-124087126	Hela-S3	cervix:	n/a	n/a
4	ELF1	chr12:124085967-124087129	GM12878	blood:	n/a	chr12:124086187-124086198 chr12:124086188-124086197 chr12:124086623-124086632
5	ZNF263	chr12:124086212-124087425	HEK293-T-REx	kidney:	n/a	n/a
6	POLR2A	chr12:124086075-124087022	GM18526	blood:	n/a	n/a
7	POLR2A	chr12:124085974-124087791	GM12878	blood:	n/a	n/a
8	MAX	chr12:124085933-124087113	HepG2	liver:	n/a	chr12:124086817-124086826
9	CREB1	chr12:124086125-124087131	K562	blood:	n/a	n/a
10	CEBPB	chr12:124086157-124087568	Hela-S3	cervix:	n/a	n/a
11	MAX	chr12:124086020-124087133	ECC-1	luminal epithelium:	n/a	chr12:124086817-124086826
12	POLR2A	chr12:124085984-124087045	GM12891	blood:	n/a	n/a
13	ETS1	chr12:124086001-124087063	A549	lung:	n/a	chr12:124086499-124086510 chr12:124086624-124086633 chr12:124086624-124086635 chr12:124086187-124086196
14	GABPA	chr12:124086095-124087080	GM12878	blood:	n/a	chr12:124086623-124086630
15	POLR2A	chr12:124086016-124087172	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr12:124085930-124087374	GM12892	blood:	n/a	n/a
17	TCF12	chr12:124086085-124087250	MCF-7	breast:	n/a	chr12:124086938-124086948
18	MAX	chr12:124086094-124087078	SK-N-SH	brain:	n/a	chr12:124086817-124086826
19	POLR2A	chr12:124085971-124087901	PFSK-1	brain:	n/a	n/a
20	MXI1	chr12:124086047-124087452	GM12878	blood:	n/a	n/a
21	POLR2A	chr12:124086116-124087029	K562	blood:	n/a	n/a
22	CHD1	chr12:124086104-124087118	GM12878	blood:	n/a	n/a
23	POLR2A	chr12:124085925-124087090	Hela-S3	cervix:	n/a	n/a
24	BCL3	chr12:124086065-124087008	A549	lung:	n/a	chr12:124086624-124086633 chr12:124086602-124086615 chr12:124086961-124086974 chr12:124086462-124086470 chr12:124086499-124086512
25	MAX	chr12:124086139-124087087	K562	blood:	n/a	chr12:124086817-124086826
26	MAX	chr12:124086086-124087110	GM12878	blood:	n/a	chr12:124086817-124086826
27	CREB1	chr12:124086181-124087052	A549	lung:	n/a	n/a
28	POLR2A	chr12:124085911-124087167	K562	blood:	n/a	n/a
29	POLR2A	chr12:124086048-124087054	HL-60	blood:	n/a	n/a
30	POLR2A	chr12:124086093-124087019	GM12891	blood:	n/a	n/a
31	SIN3AK20	chr12:124085994-124087139	PANC-1	pancreas:	n/a	n/a
32	MAX	chr12:124085987-124087133	ECC-1	luminal epithelium:	n/a	chr12:124086817-124086826
33	MAX	chr12:124086019-124087098	H1-hESC	embryonic stem cell:	n/a	chr12:124086817-124086826
34	GABPA	chr12:124085968-124087300	MCF-7	breast:	n/a	chr12:124086623-124086630
35	POLR2A	chr12:124086060-124087008	HUVEC	blood vessel:	n/a	n/a
36	ELF1	chr12:124085915-124087065	MCF-7	breast:	n/a	chr12:124086187-124086198 chr12:124086188-124086197 chr12:124086623-124086632
37	GABPA	chr12:124085912-124087324	A549	lung:	n/a	chr12:124086623-124086630
38	SIX5	chr12:124085841-124087006	A549	lung:	n/a	n/a
39	TBL1XR1	chr12:124086072-124087181	K562	blood:	n/a	n/a
40	POLR2A	chr12:124085980-124087032	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr12:124086155-124087111	ProgFib	skin:	n/a	n/a
42	POLR2A	chr12:124086190-124087014	HUVEC	blood vessel:	n/a	n/a
43	MXI1	chr12:124086113-124087036	HepG2	liver:	n/a	n/a
44	REST	chr12:124086010-124087054	HL-60	blood:	n/a	chr12:124086966-124086979 chr12:124086498-124086511 chr12:124086334-124086347 chr12:124086459-124086469
45	MYC	chr12:124086096-124087513	NB4	blood:	n/a	chr12:124086817-124086826
46	SP1	chr12:124085943-124087051	A549	lung:	n/a	chr12:124086832-124086846 chr12:124087005-124087014 chr12:124087004-124087013 chr12:124087003-124087015 chr12:124087005-124087018 chr12:124087003-124087015 chr12:124087004-124087014
47	POLR2A	chr12:124086005-124087349	GM18505	blood:	n/a	n/a
48	PML	chr12:124086297-124087009	MCF-7	breast:	n/a	n/a
49	GABPA	chr12:124085977-124087232	SK-N-SH	brain:	n/a	chr12:124086623-124086630
50	POLR2A	chr12:124085718-124087673	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	chr12:57824029..57824578-chr12:124086334..124087217,2	Hela-S3	cervix:
7	chr12:124084914..124087862-chr12:124122413..124125179,2	K562	blood:
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	chr12:124084644..124087346-chr12:124096148..124098451,3	K562	blood:
19	chr12:124086664..124088557-chr12:124117448..124120033,4	K562	blood:
20	chr12:123847169..123849970-chr12:124085128..124088523,3	K562	blood:
21	chr12:123867386..123869300-chr12:124085669..124087822,2	K562	blood:

Variant related genes	Relation type
DDX55	TF binding region
ENSG00000111361	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000184209	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000247373	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000179912	Chromatin interaction
ENSG00000206897	Chromatin interaction
ENSG00000256092	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11057298	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11057302	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057306	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11572931	1.00[JPT][hapmap]
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];1.00[JPT][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];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2340691	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28694725	1.00[JPT][hapmap]
rs3209852	0.81[ASN][1000 genomes]
rs34099549	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748268	0.89[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	0.85[CEU][hapmap]
rs6488881	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
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];1.00[JPT][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]
rs786429	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	1.00[JPT][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[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[JPT][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	0.88[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];1.00[JPT][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]
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];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs884892	0.89[CEU][hapmap]
rs952360	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs786428	DDX55	cis	Thyroid	GTEx
rs786428	RP11-486O12.2	cis	Thyroid	GTEx
rs786428	RP11-486O12.2	cis	Adipose Subcutaneous	GTEx
rs786428	RP11-486O12.2	cis	Esophagus Muscularis	GTEx
rs786428	RP11-486O12.2	cis	Heart Left Ventricle	GTEx
rs786428	DDX55	cis	Esophagus Muscularis	GTEx
rs786428	RP11-486O12.2	cis	Muscle Skeletal	GTEx
rs786428	RP11-486O12.2	cis	Esophagus Mucosa	GTEx
rs786428	DDX55	cis	Frontal Cortex	GTEx
rs786428	DDX55	cis	lung	GTEx
rs786428	RP11-486O12.2	cis	Nerve Tibial	GTEx
rs786428	DDX55	cis	Brain Pons	GTEx
rs786428	RP11-486O12.2	cis	Artery Aorta	GTEx
rs786428	ENSG00000111364	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124085400-124087200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:124085400-124087200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:124085400-124087200	Active TSS	Rectal Smooth Muscle	rectum
4	chr12:124085400-124087400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:124085400-124087800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:124085600-124087000	Active TSS	Rectal Mucosa Donor 31	rectum
7	chr12:124085600-124087200	Active TSS	Primary T cells from cord blood	blood
8	chr12:124085600-124087200	Active TSS	Brain Hippocampus Middle	brain
9	chr12:124085600-124087200	Active TSS	Colonic Mucosa	Colon
10	chr12:124085600-124087400	Active TSS	Muscle Satellite Cultured Cells	--
11	chr12:124085600-124087400	Active TSS	HSMM	muscle
12	chr12:124085600-124087400	Active TSS	NHLF	lung
13	chr12:124085600-124087600	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr12:124085600-124087600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:124085600-124087600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:124085600-124087800	Active TSS	Fetal Kidney	kidney
17	chr12:124085600-124088000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:124085600-124088000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:124085600-124088000	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr12:124085600-124088000	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr12:124085600-124088000	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr12:124085600-124088400	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr12:124085600-124088400	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr12:124085800-124087000	Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr12:124085800-124087000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:124085800-124087000	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr12:124085800-124087000	Active TSS	Hela-S3	cervix
28	chr12:124085800-124087200	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr12:124085800-124087200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr12:124085800-124087200	Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr12:124085800-124087200	Active TSS	Thymus	Thymus
32	chr12:124085800-124087400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:124085800-124087400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:124085800-124087400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:124085800-124087400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:124085800-124087400	Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr12:124085800-124087400	Active TSS	Colon Smooth Muscle	Colon
38	chr12:124085800-124087400	Active TSS	Fetal Lung	lung
39	chr12:124085800-124087400	Active TSS	Left Ventricle	heart
40	chr12:124085800-124087400	Active TSS	Pancreas	Pancrea
41	chr12:124085800-124087400	Active TSS	HSMMtube	muscle
42	chr12:124085800-124087400	Active TSS	K562	blood
43	chr12:124085800-124087400	Active TSS	NHEK	skin
44	chr12:124085800-124087400	Active TSS	Osteobl	bone
45	chr12:124085800-124087600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:124085800-124087600	Active TSS	Esophagus	oesophagus
47	chr12:124085800-124087600	Active TSS	Right Atrium	heart
48	chr12:124085800-124088000	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr12:124085800-124088000	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr12:124085800-124088000	Active TSS	A549	lung

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