Variant report

Variant	rs12828755
Chromosome Location	chr12:123470586-123470587
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:123466333-123470624	K562	blood:	n/a	n/a
2	GABPA	chr12:123470529-123470840	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr12:123470098-123470872	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:123470093-123471163	A549	lung:	n/a	n/a
5	POLR2A	chr12:123469118-123470607	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123469090..123471551-chr12:123505815..123507895,2	MCF-7	breast:
2	chr12:123467378..123471463-chr12:123484194..123486166,3	MCF-7	breast:
3	chr12:123470053..123472975-chr12:123718822..123721771,2	K562	blood:
4	chr12:123468471..123472230-chr12:123634537..123637693,4	K562	blood:
5	chr12:123469032..123471248-chr12:123684974..123687831,2	K562	blood:
6	chr12:123470251..123473502-chr12:123478198..123482037,4	MCF-7	breast:
7	chr12:123469171..123471248-chr12:123684974..123686845,2	K562	blood:
8	chr12:123467368..123470978-chr12:123525099..123527744,3	K562	blood:

No data

Variant related genes	Relation type
ABCB9	TF binding region
ENSG00000090975	Chromatin interaction
ENSG00000051825	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12811109	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12820906	0.83[EUR][1000 genomes]
rs1463877	0.96[EUR][1000 genomes]
rs4148856	0.91[EUR][1000 genomes]
rs520088	0.87[EUR][1000 genomes]
rs585522	0.81[EUR][1000 genomes]
rs655293	0.87[EUR][1000 genomes]
rs71444568	0.87[EUR][1000 genomes]
rs883263	0.96[EUR][1000 genomes]
rs883563	0.91[EUR][1000 genomes]
rs937564	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
13	nsv560493	chr12:123467325-123479623	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12828755	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs12828755	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs12828755	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs12828755	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs12828755	CDK2AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs12828755	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs12828755	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs12828755	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123461400-123473200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:123466400-123473400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:123466600-123470600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr12:123466600-123471400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:123466600-123483400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:123466800-123471000	Genic enhancers	Liver	Liver
7	chr12:123466800-123472000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:123466800-123472400	Genic enhancers	Spleen	Spleen
9	chr12:123466800-123516000	Weak transcription	Small Intestine	intestine
10	chr12:123467000-123474000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:123467400-123472000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:123467600-123504000	Weak transcription	Hela-S3	cervix
13	chr12:123468000-123486200	Strong transcription	Fetal Brain Female	brain
14	chr12:123468200-123470600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:123468200-123470800	Weak transcription	Dnd41	blood
16	chr12:123468200-123471400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr12:123468200-123471800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr12:123468200-123476800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:123468200-123477800	Strong transcription	Brain Germinal Matrix	brain
20	chr12:123468600-123471600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr12:123468800-123471000	Strong transcription	Thymus	Thymus
22	chr12:123468800-123471400	Weak transcription	Primary B cells from cord blood	blood
23	chr12:123468800-123477000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr12:123468800-123485200	Weak transcription	Aorta	Aorta
25	chr12:123469000-123471800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr12:123469000-123472800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr12:123469000-123476600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:123469200-123477400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr12:123469200-123498600	Strong transcription	Primary T cells from cord blood	blood
30	chr12:123469400-123471000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr12:123469400-123473000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:123469400-123473800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:123469400-123479400	Weak transcription	Psoas Muscle	Psoas
34	chr12:123469400-123491600	Weak transcription	HMEC	breast
35	chr12:123469400-123509400	Weak transcription	NHDF-Ad	bronchial
36	chr12:123469400-123509600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr12:123469600-123470600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr12:123469600-123470600	Genic enhancers	Stomach Smooth Muscle	stomach
39	chr12:123469600-123471000	Genic enhancers	Brain Anterior Caudate	brain
40	chr12:123469600-123471600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr12:123469600-123473800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr12:123469600-123474000	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr12:123469600-123474800	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr12:123469600-123475200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr12:123469600-123475200	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr12:123469600-123475600	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr12:123469600-123477000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr12:123469600-123477000	Strong transcription	Colonic Mucosa	Colon
49	chr12:123469600-123484600	Weak transcription	Primary B cells from peripheral blood	blood
50	chr12:123469600-123493200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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