Variant report

Variant	rs2278094
Chromosome Location	chr12:29534492-29534493
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	TBP	chr12:29533431-29534998	Hela-S3	cervix:	n/a	n/a
2	ARID3A	chr12:29534028-29534942	K562	blood:	n/a	n/a
3	TAF1	chr12:29533193-29534722	ECC-1	luminal epithelium:	n/a	n/a
4	RELA	chr12:29533339-29534514	GM19099	blood:	n/a	n/a
5	MXI1	chr12:29533401-29534522	HepG2	liver:	n/a	n/a
6	MAFK	chr12:29534044-29534670	HepG2	liver:	n/a	n/a
7	RUNX3	chr12:29533408-29534595	GM12878	blood:	n/a	n/a
8	MAX	chr12:29533266-29534593	A549	lung:	n/a	n/a
9	FOS	chr12:29534037-29534520	MCF10A-Er-Src	breast:	n/a	chr12:29534345-29534357
10	POLR2A	chr12:29533085-29534613	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr12:29533343-29534524	GM12891	blood:	n/a	n/a
12	POLR2A	chr12:29533818-29534543	HCT-116	colon:	n/a	n/a
13	POLR2A	chr12:29533270-29534663	SK-N-SH	brain:	n/a	n/a
14	MAFK	chr12:29533332-29534729	K562	blood:	n/a	n/a
15	POLR2A	chr12:29533386-29534560	Raji	blood:	n/a	n/a
16	ZBTB33	chr12:29533465-29534560	SK-N-SH	brain:	n/a	chr12:29534183-29534192 chr12:29534117-29534132 chr12:29534122-29534131
17	CREB1	chr12:29533731-29534543	K562	blood:	n/a	n/a
18	MAX	chr12:29533228-29534492	MCF-7	breast:	n/a	n/a
19	TCF12	chr12:29533208-29534653	ECC-1	luminal epithelium:	n/a	n/a
20	IRF1	chr12:29533871-29534635	K562	blood:	n/a	chr12:29534475-29534485 chr12:29534471-29534485 chr12:29534479-29534499 chr12:29534475-29534489
21	POLR2A	chr12:29533332-29534609	GM19193	blood:	n/a	n/a
22	POLR2A	chr12:29533841-29534512	HCT-116	colon:	n/a	n/a
23	MAX	chr12:29533217-29534641	A549	lung:	n/a	n/a
24	HEY1	chr12:29533797-29534578	HepG2	liver:	n/a	n/a
25	NFYA	chr12:29534022-29534557	Hela-S3	cervix:	n/a	n/a
26	CHD2	chr12:29533484-29534614	K562	blood:	n/a	chr12:29534183-29534192 chr12:29534122-29534131
27	POLR2A	chr12:29533165-29534613	HUVEC	blood vessel:	n/a	n/a
28	MAX	chr12:29533925-29534495	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr12:29533357-29534502	GM12891	blood:	n/a	n/a
30	RCOR1	chr12:29533357-29534992	K562	blood:	n/a	n/a
31	POLR2A	chr12:29533231-29534626	ECC-1	luminal epithelium:	n/a	n/a
32	FOXM1	chr12:29533475-29534495	GM12878	blood:	n/a	n/a
33	TAF1	chr12:29533687-29534492	GM12878	blood:	n/a	n/a
34	MAX	chr12:29533238-29534556	Hela-S3	cervix:	n/a	n/a
35	HCFC1	chr12:29532464-29535072	Hela-S3	cervix:	n/a	n/a
36	SMC3	chr12:29533311-29534661	Hela-S3	cervix:	n/a	n/a
37	RCOR1	chr12:29533388-29534582	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr12:29533584-29534586	SK-N-MC	brain:	n/a	n/a
39	POLR2A	chr12:29533379-29534709	PFSK-1	brain:	n/a	n/a
40	POLR2A	chr12:29533360-29534502	K562	blood:	n/a	n/a
41	SIN3A	chr12:29533195-29534530	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr12:29533258-29534523	GM12891	blood:	n/a	n/a
43	KAP1	chr12:29533460-29534654	HEK293	kidney:	n/a	n/a
44	GATA3	chr12:29533303-29534566	SK-N-SH	brain:	n/a	chr12:29533944-29533952 chr12:29534238-29534249
45	STAT3	chr12:29533338-29534609	MCF10A-Er-Src	breast:	n/a	chr12:29533526-29533538 chr12:29534322-29534334
46	ZBTB33	chr12:29533346-29534502	HCT-116	colon:	n/a	chr12:29534183-29534192 chr12:29534117-29534132 chr12:29534122-29534131
47	POLR2A	chr12:29533818-29534558	HepG2	liver:	n/a	n/a
48	POLR2A	chr12:29533360-29534560	GM18526	blood:	n/a	n/a
49	POLR2A	chr12:29533913-29534519	HepG2	liver:	n/a	n/a
50	POLR2A	chr12:29533436-29534594	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:29534107..29534768-chr16:18800798..18801625,2	Hela-S3	cervix:
2	chr12:29534019..29534774-chr12:125401581..125402432,2	Hela-S3	cervix:
3	chr11:47869535..47870067-chr12:29533757..29534605,2	HCT-116	colon:
4	chr12:29534214..29536521-chr12:29538492..29540922,3	K562	blood:

Variant related genes	Relation type
ERGIC2	TF binding region
ENSG00000150991	Chromatin interaction
ENSG00000030066	Chromatin interaction
ENSG00000134419	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10082956	0.81[AFR][1000 genomes]
rs10128781	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1035606	1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10743657	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743658	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843390	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10843391	1.00[LWK][hapmap];0.85[MKK][hapmap];0.87[YRI][hapmap]
rs10843397	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs10843398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10843403	0.81[CEU][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10843407	0.80[ASN][1000 genomes]
rs11050203	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs11050209	0.82[AFR][1000 genomes]
rs1156242	0.81[AFR][1000 genomes]
rs12228468	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12831751	1.00[LWK][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs1989478	0.90[ASN][1000 genomes]
rs2194515	0.80[ASN][1000 genomes]
rs2278093	1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs3782513	1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs3815843	0.91[YRI][hapmap]
rs3847678	0.91[CHB][hapmap];0.86[CHD][hapmap];0.80[ASN][1000 genomes]
rs4931177	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4931178	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6487804	0.83[ASN][1000 genomes]
rs6487813	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6487815	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487818	0.81[ASN][1000 genomes]
rs7139273	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs7297435	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7302557	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311742	0.83[AFR][1000 genomes]
rs7315504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737160	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs962866	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs9651802	0.81[AFR][1000 genomes]
rs966540	0.82[AFR][1000 genomes]
rs996498	1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs9989017	1.00[YRI][hapmap];0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2278094	RASSF8	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29531000-29535200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:29531600-29534800	Active TSS	GM12878-XiMat	blood
3	chr12:29532200-29534600	Active TSS	HSMMtube	muscle
4	chr12:29532200-29535200	Active TSS	HMEC	breast
5	chr12:29532600-29534600	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr12:29532600-29534800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:29532600-29534800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:29532600-29534800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:29532600-29534800	Active TSS	Brain Anterior Caudate	brain
10	chr12:29532600-29534800	Active TSS	Colon Smooth Muscle	Colon
11	chr12:29532600-29535000	Active TSS	K562	blood
12	chr12:29532600-29535200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:29532800-29534800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:29532800-29534800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:29532800-29534800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:29532800-29534800	Active TSS	Muscle Satellite Cultured Cells	--
17	chr12:29532800-29534800	Active TSS	Right Ventricle	heart
18	chr12:29532800-29534800	Active TSS	Hela-S3	cervix
19	chr12:29532800-29534800	Active TSS	NH-A	brain
20	chr12:29532800-29534800	Active TSS	NHDF-Ad	bronchial
21	chr12:29532800-29535000	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr12:29532800-29535000	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr12:29532800-29535000	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr12:29532800-29535000	Active TSS	Colonic Mucosa	Colon
25	chr12:29532800-29535000	Active TSS	Fetal Intestine Large	intestine
26	chr12:29533000-29534600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:29533000-29534600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:29533000-29534600	Active TSS	Brain Angular Gyrus	brain
29	chr12:29533000-29534600	Active TSS	HSMM	muscle
30	chr12:29533000-29534800	Active TSS	H1 Cell Line	embryonic stem cell
31	chr12:29533000-29534800	Active TSS	H9 Cell Line	embryonic stem cell
32	chr12:29533000-29534800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:29533000-29534800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:29533000-29534800	Active TSS	Aorta	Aorta
35	chr12:29533000-29534800	Active TSS	Brain Cingulate Gyrus	brain
36	chr12:29533000-29534800	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr12:29533000-29534800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:29533000-29534800	Active TSS	Brain Substantia Nigra	brain
39	chr12:29533000-29534800	Active TSS	Fetal Intestine Small	intestine
40	chr12:29533000-29534800	Active TSS	Fetal Muscle Trunk	muscle
41	chr12:29533000-29534800	Active TSS	Fetal Stomach	stomach
42	chr12:29533000-29534800	Active TSS	Psoas Muscle	Psoas
43	chr12:29533000-29534800	Active TSS	Right Atrium	heart
44	chr12:29533000-29535000	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr12:29533200-29534600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr12:29533200-29534600	Active TSS	Left Ventricle	heart
47	chr12:29533200-29534600	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr12:29533200-29534600	Active TSS	Thymus	Thymus
49	chr12:29533200-29534800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr12:29533200-29534800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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