Variant report

Variant	rs884956
Chromosome Location	chr12:123460962-123460963
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:123458534-123466263	K562	blood:	n/a	n/a
2	POLR2A	chr12:123458680-123461169	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr12:123458851-123461232	K562	blood:	n/a	n/a
4	POLR2A	chr12:123458643-123461407	HL-60	blood:	n/a	n/a
5	POLR2A	chr12:123458841-123461033	Raji	blood:	n/a	n/a
6	POLR2A	chr12:123460872-123461345	HepG2	liver:	n/a	n/a
7	GATA1	chr12:123458879-123460996	PBDE	blood:	n/a	n/a
8	TEAD4	chr12:123458672-123461113	K562	blood:	n/a	n/a
9	POLR2A	chr12:123460287-123466106	K562	blood:	n/a	n/a
10	POLR2A	chr12:123458704-123461070	GM12891	blood:	n/a	n/a
11	POLR2A	chr12:123458554-123460986	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr12:123458693-123461033	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr12:123458558-123461092	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr12:123458747-123460980	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr12:123458863-123461074	GM12878	blood:	n/a	n/a
16	JUN	chr12:123458446-123461591	K562	blood:	n/a	chr12:123460542-123460551
17	POLR2A	chr12:123458769-123461278	PFSK-1	brain:	n/a	n/a
18	POLR2A	chr12:123458541-123460989	ECC-1	luminal epithelium:	n/a	n/a
19	HEY1	chr12:123458854-123461109	K562	blood:	n/a	n/a
20	POLR2A	chr12:123458662-123461154	HepG2	liver:	n/a	n/a
21	POLR2A	chr12:123458588-123461084	PANC-1	pancreas:	n/a	n/a
22	POLR2A	chr12:123458343-123460972	HepG2	liver:	n/a	n/a
23	POLR2A	chr12:123458525-123461675	K562	blood:	n/a	n/a
24	POLR2A	chr12:123458736-123461084	MCF-7	breast:	n/a	n/a
25	ZNF263	chr12:123459078-123461051	HEK293-T-REx	kidney:	n/a	chr12:123460830-123460839 chr12:123460535-123460544 chr12:123460833-123460842 chr12:123460827-123460836
26	POLR2A	chr12:123458623-123461051	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123459054..123462367-chr12:123715409..123720380,5	K562	blood:
2	chr12:123458067..123461017-chr12:123715728..123717607,2	MCF-7	breast:
3	chr12:123458147..123462549-chr12:123715608..123720287,8	MCF-7	breast:
4	chr12:123444682..123447187-chr12:123459178..123461063,2	K562	blood:
5	chr12:120728398..120730404-chr12:123459731..123462257,2	MCF-7	breast:
6	chr12:123433587..123436454-chr12:123458977..123461529,2	K562	blood:
7	chr12:123344929..123347895-chr12:123458197..123461633,3	MCF-7	breast:
8	chr12:123344672..123346333-chr12:123459122..123461016,2	MCF-7	breast:
9	chr12:123457894..123461734-chr12:123715409..123718960,7	K562	blood:
10	chr12:123353599..123356535-chr12:123459324..123461652,2	MCF-7	breast:

No data

Variant related genes	Relation type
OGFOD2	TF binding region
ARL6IP4	TF binding region
ABCB9	TF binding region
ENSG00000150967	Chromatin interaction
ENSG00000139722	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000202538	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1051434	0.87[MEX][hapmap];1.00[YRI][hapmap]
rs10773921	1.00[ASW][hapmap];0.95[CHB][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10848428	1.00[ASW][hapmap];0.95[CHB][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]
rs11060853	0.84[ASN][1000 genomes]
rs11608811	0.90[ASW][hapmap];0.95[CHB][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11613937	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12425009	0.90[ASW][hapmap];0.95[CHB][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12425850	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1615350	0.83[ASW][hapmap]
rs1727293	1.00[ASW][hapmap];0.86[CHB][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs1727295	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs1727307	0.95[CHB][hapmap]
rs1790094	0.90[ASW][hapmap];0.95[CHB][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]
rs1790106	1.00[ASW][hapmap];0.95[CHB][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]
rs1790121	0.90[ASW][hapmap];0.95[CHB][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap]
rs1984658	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28755851	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3741530	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3759115	1.00[ASW][hapmap];0.95[CHB][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3897102	0.95[CHB][hapmap];0.98[ASN][1000 genomes]
rs4148862	0.80[EUR][1000 genomes]
rs4148863	0.90[ASW][hapmap];0.95[CHB][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs4148866	0.83[ASN][1000 genomes]
rs4275659	1.00[ASW][hapmap];0.90[CHB][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55742290	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61955196	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61955214	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7135296	1.00[ASW][hapmap];0.95[CHB][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7296418	0.90[CHB][hapmap];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7305511	1.00[ASW][hapmap];0.95[CHB][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7957096	0.84[CHB][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs883562	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs949143	1.00[ASW][hapmap];0.95[CHB][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
9	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv899577	chr12:123435248-123484474	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
12	nsv899578	chr12:123459005-123474529	Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs884956	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs884956	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs884956	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs884956	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs884956	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs884956	CDK2AP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123458400-123461200	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr12:123458600-123461000	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr12:123458600-123461000	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr12:123459800-123461000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr12:123459800-123461400	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr12:123459800-123461400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:123459800-123461600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
8	chr12:123460000-123461000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
9	chr12:123460000-123461000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr12:123460000-123461000	Flanking Active TSS	Brain Germinal Matrix	brain
11	chr12:123460000-123461000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr12:123460000-123461400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:123460000-123461400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:123460000-123461400	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr12:123460000-123461400	Flanking Active TSS	Liver	Liver
16	chr12:123460200-123461000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr12:123460200-123461000	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr12:123460200-123461000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr12:123460200-123461000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr12:123460200-123461000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr12:123460200-123461000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr12:123460200-123461000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:123460200-123461000	Flanking Active TSS	Esophagus	oesophagus
24	chr12:123460200-123461000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr12:123460200-123461000	Flanking Active TSS	Fetal Muscle Trunk	muscle
26	chr12:123460200-123461000	Flanking Active TSS	Fetal Thymus	thymus
27	chr12:123460200-123461000	Flanking Active TSS	Thymus	Thymus
28	chr12:123460200-123461000	Flanking Active TSS	HUVEC	blood vessel
29	chr12:123460200-123461200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:123460200-123461200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:123460200-123461200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:123460200-123461200	Flanking Active TSS	Brain Angular Gyrus	brain
33	chr12:123460200-123461200	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr12:123460200-123461200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
35	chr12:123460200-123461200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:123460200-123461200	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr12:123460200-123461200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr12:123460200-123461200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr12:123460200-123461200	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr12:123460200-123461200	Flanking Active TSS	Hela-S3	cervix
41	chr12:123460200-123461200	Flanking Active TSS	K562	blood
42	chr12:123460200-123461400	Flanking Active TSS	Colonic Mucosa	Colon
43	chr12:123460200-123461400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr12:123460200-123461600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:123460200-123461600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:123460200-123461600	Flanking Active TSS	Duodenum Mucosa	Duodenum
47	chr12:123460400-123461000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:123460400-123461000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr12:123460400-123461000	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr12:123460400-123461000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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