Variant report

Variant	rs11057302
Chromosome Location	chr12:124070013-124070014
allele	A/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	chr12:124068520-124070709	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr12:124069627-124073859	K562	blood:	n/a	n/a
3	CEBPB	chr12:124070005-124070446	HepG2	liver:	n/a	chr12:124070264-124070281 chr12:124070266-124070277 chr12:124070265-124070276
4	POLR2A	chr12:124069686-124070761	GM12878	blood:	n/a	n/a
5	CEBPB	chr12:124070004-124070702	IMR90	lung:	n/a	chr12:124070264-124070281 chr12:124070266-124070277 chr12:124070265-124070276
6	SIN3A	chr12:124068728-124070099	H1-hESC	embryonic stem cell:	n/a	n/a
7	TAL1	chr12:124069980-124070223	K562	blood:	n/a	n/a
8	MAX	chr12:124068442-124070037	A549	lung:	n/a	n/a
9	MXI1	chr12:124068488-124070795	IMR90	lung:	n/a	n/a
10	UBTF	chr12:124068570-124070035	K562	blood:	n/a	n/a
11	MAX	chr12:124068731-124070113	K562	blood:	n/a	n/a
12	POLR2A	chr12:124069625-124070734	PFSK-1	brain:	n/a	n/a
13	HCFC1	chr12:124068422-124070407	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr12:124068496-124070077	K562	blood:	n/a	n/a
15	POLR2A	chr12:124069888-124070634	K562	blood:	n/a	n/a
16	POLR2A	chr12:124068404-124070969	HepG2	liver:	n/a	n/a
17	MXI1	chr12:124068656-124070224	GM12878	blood:	n/a	n/a
18	CEBPB	chr12:124069973-124070401	Hela-S3	cervix:	n/a	chr12:124070264-124070281 chr12:124070266-124070277 chr12:124070265-124070276
19	POLR2A	chr12:124067817-124070121	HepG2	liver:	n/a	n/a
20	POLR2A	chr12:124069581-124070124	PFSK-1	brain:	n/a	n/a
21	PML	chr12:124069588-124070488	K562	blood:	n/a	n/a
22	CEBPB	chr12:124070009-124070436	A549	lung:	n/a	chr12:124070264-124070281 chr12:124070266-124070277 chr12:124070265-124070276
23	POLR2A	chr12:124068344-124070778	MCF10A-Er-Src	breast:	n/a	n/a
24	MAX	chr12:124068613-124070033	K562	blood:	n/a	n/a
25	POLR2A	chr12:124067815-124070088	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr12:124068640-124070455	GM12878	blood:	n/a	n/a
27	POLR2A	chr12:124069683-124070910	HepG2	liver:	n/a	n/a
28	REST	chr12:124068463-124070041	A549	lung:	n/a	chr12:124069466-124069475
29	CHD1	chr12:124068312-124070779	IMR90	lung:	n/a	chr12:124069693-124069700
30	POLR2A	chr12:124068407-124070326	MCF10A-Er-Src	breast:	n/a	n/a
31	JUN	chr12:124068570-124070748	K562	blood:	n/a	chr12:124070434-124070446
32	MXI1	chr12:124067740-124070353	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr12:124068549-124070907	IMR90	lung:	n/a	n/a
34	CEBPB	chr12:124069886-124070492	A549	lung:	n/a	chr12:124070264-124070281 chr12:124070266-124070277 chr12:124070265-124070276
35	MAZ	chr12:124068549-124070932	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:123846000..123850093-chr12:124067189..124070124,4	K562	blood:
2	chr12:123755285..123757528-chr12:124068793..124071301,3	MCF-7	breast:
3	chr12:123941098..123944051-chr12:124068238..124070527,2	K562	blood:
4	chr12:124067567..124070616-chr12:124116717..124118360,3	K562	blood:
5	chr12:124067302..124072457-chr12:124084684..124088760,8	K562	blood:
6	chr12:124068831..124072178-chr12:124116882..124120107,5	K562	blood:
7	chr12:124067363..124072745-chr12:124084857..124088217,7	K562	blood:
8	chr12:123941578..123944282-chr12:124067320..124071098,9	MCF-7	breast:
9	chr12:123846861..123850261-chr12:124066655..124071408,9	MCF-7	breast:
10	chr12:124067553..124070106-chr12:124116767..124119854,4	MCF-7	breast:
11	chr12:124016749..124018606-chr12:124069216..124071514,2	K562	blood:
12	chr12:123847713..123850022-chr12:124067528..124071055,3	MCF-7	breast:
13	chr12:123753500..123755086-chr12:124068992..124070507,2	MCF-7	breast:
14	chr12:124018224..124020563-chr12:124065688..124070487,5	K562	blood:
15	chr12:123872778..123876196-chr12:124065295..124071344,6	MCF-7	breast:

Variant related genes	Relation type
TMED2	TF binding region
ENSG00000247373	TF binding region
ENSG00000111364	Chromatin interaction
ENSG00000188026	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000111361	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000184209	Chromatin interaction
ENSG00000111328	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11057298	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11057306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11572931	1.00[JPT][hapmap]
rs11610013	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615043	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11829661	0.84[AFR][1000 genomes]
rs11834369	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837236	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12099981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12099985	0.90[AFR][1000 genomes]
rs12099986	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877365	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2340691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28540654	1.00[JPT][hapmap]
rs28691687	0.89[MEX][hapmap]
rs28694725	1.00[JPT][hapmap]
rs3209852	0.81[ASN][1000 genomes]
rs34099549	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748268	0.90[CEU][hapmap]
rs3850953	0.88[AFR][1000 genomes]
rs4930715	0.96[EUR][1000 genomes]
rs61678733	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488879	0.86[CEU][hapmap]
rs6488881	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6488882	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs7136101	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7137130	0.85[YRI][hapmap]
rs7301377	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303554	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];1.00[MKK][hapmap];1.00[TSI][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]
rs7316613	0.94[EUR][1000 genomes]
rs73414262	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs786428	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786429	1.00[CEU][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786431	1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786432	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786433	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786434	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786435	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786437	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786438	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786450	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786455	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs7954782	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7958153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960812	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964934	0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs7965292	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7965466	0.84[EUR][1000 genomes]
rs7968040	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970545	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971779	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973187	0.88[AFR][1000 genomes]
rs7973689	0.83[ASW][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs884892	0.90[CEU][hapmap]
rs952360	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];1.00[MKK][hapmap];1.00[TSI][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]
rs9697379	0.89[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	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:21)

SNP	Gene	Cis/trans	Tissue	Source
rs11057302	RP11-486O12.2	cis	Adipose Subcutaneous	GTEx
rs11057302	TCTN2	cis	cerebellum	SCAN
rs11057302	DDX55	cis	parietal	SCAN
rs11057302	DDX55	cis	cerebellum	SCAN
rs11057302	DDX55	cis	lung	GTEx
rs11057302	DDX55	cis	Esophagus Muscularis	GTEx
rs11057302	RP11-486O12.2	cis	Esophagus Muscularis	GTEx
rs11057302	RP11-486O12.2	cis	Artery Aorta	GTEx
rs11057302	DDX55	cis	Frontal Cortex	GTEx
rs11057302	RP11-486O12.2	cis	Esophagus Mucosa	GTEx
rs11057302	TAOK3	cis	cerebellum	SCAN
rs11057302	RP11-486O12.2	cis	Thyroid	GTEx
rs11057302	DDX55	cis	Brain Pons	GTEx
rs11057302	RP11-486O12.2	cis	Muscle Skeletal	GTEx
rs11057302	DDX55	cis	multi-tissue	Pritchard
rs11057302	PXN	cis	cerebellum	SCAN
rs11057302	RP11-486O12.2	cis	Nerve Tibial	GTEx
rs11057302	RP11-486O12.2	cis	Heart Left Ventricle	GTEx
rs11057302	DDX55	cis	Thyroid	GTEx
rs11057302	SNRNP35	cis	parietal	SCAN
rs11057302	MPHOSPH9	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124067000-124070400	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr12:124067200-124070400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:124067200-124070600	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr12:124067400-124070200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:124067400-124070200	Active TSS	A549	lung
6	chr12:124067400-124070800	Active TSS	NHLF	lung
7	chr12:124067600-124070200	Active TSS	H1 Cell Line	embryonic stem cell
8	chr12:124067600-124070200	Active TSS	Aorta	Aorta
9	chr12:124067600-124070200	Active TSS	Fetal Intestine Large	intestine
10	chr12:124067600-124070400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:124067600-124070400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:124067600-124071400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:124068000-124070200	Active TSS	Fetal Intestine Small	intestine
14	chr12:124068000-124070200	Active TSS	Gastric	stomach
15	chr12:124068000-124070200	Active TSS	Left Ventricle	heart
16	chr12:124068000-124070200	Active TSS	Pancreas	Pancrea
17	chr12:124068000-124070200	Active TSS	Psoas Muscle	Psoas
18	chr12:124068000-124070600	Active TSS	Right Ventricle	heart
19	chr12:124068200-124070200	Active TSS	Fetal Muscle Trunk	muscle
20	chr12:124069400-124070200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
21	chr12:124069400-124070400	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr12:124069400-124070400	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr12:124069400-124070600	Active TSS	Right Atrium	heart
24	chr12:124069600-124070200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
25	chr12:124069600-124070200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr12:124069600-124070200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
27	chr12:124069600-124070200	Flanking Active TSS	Brain Substantia Nigra	brain
28	chr12:124069600-124070200	Flanking Active TSS	Fetal Thymus	thymus
29	chr12:124069600-124070400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr12:124069600-124070400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr12:124069600-124070400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr12:124069600-124070400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr12:124069600-124070400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:124069600-124070400	Flanking Active TSS	Liver	Liver
35	chr12:124069600-124070400	Flanking Active TSS	Brain Cingulate Gyrus	brain
36	chr12:124069600-124070400	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr12:124069600-124070400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr12:124069600-124070400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr12:124069600-124070400	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr12:124069600-124070600	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr12:124069600-124070600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr12:124069600-124070600	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr12:124069600-124070600	Flanking Active TSS	Brain Germinal Matrix	brain
44	chr12:124069600-124070600	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr12:124069600-124070600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr12:124069600-124070800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:124069800-124070200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:124069800-124070200	Flanking Active TSS	Colonic Mucosa	Colon
49	chr12:124069800-124070200	Flanking Active TSS	Placenta	Placenta
50	chr12:124069800-124070400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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