Variant report

Variant	rs12811109
Chromosome Location	chr12:123471094-123471095
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
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	EGR1	chr12:123470851-123471123	K562	blood:	n/a	chr12:123470956-123470971 chr12:123470952-123470974 chr12:123470957-123470970 chr12:123470957-123470970 chr12:123470957-123470967
2	POLR2A	chr12:123471034-123471123	A549	lung:	n/a	n/a
3	POLR2A	chr12:123470929-123471173	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:123470093-123471163	A549	lung:	n/a	n/a
5	POLR2A	chr12:123470976-123471273	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:123471054-123471104	SAEC	small airway:	n/a
2	chr12:123471054-123471104	HEEpiC	esophagus:	n/a
3	chr12:123471054-123471104	SKMC	muscle:	n/a
4	chr12:123471054-123471104	HIPEpiC	eye:	n/a
5	chr12:123471054-123471104	K562	blood:	n/a
6	chr12:123471054-123471104	AG04450	lung:	fetal
7	chr12:123471054-123471104	A549	lung:	n/a
8	chr12:123471054-123471104	BE2_C	brain:	n/a
9	chr12:123471054-123471104	AG10803	skin:	n/a
10	chr12:123471054-123471104	U87	brain:	n/a
11	chr12:123471054-123471104	RPTEC	kidney:	n/a
12	chr12:123471054-123471104	HCPEpiC	choroid plexus:	n/a
13	chr12:123471054-123471104	HCM	heart:	n/a
14	chr12:123471054-123471104	HEK293	kidney:	embryo
15	chr12:123471054-123471104	NH-A	brain:	n/a
16	chr12:123471054-123471104	HRPEpiC	eye:	n/a
17	chr12:123471054-123471104	Hepatocyte	liver:	n/a
18	chr12:123471054-123471104	HL-60	blood:	n/a
19	chr12:123471054-123471104	AG09309	skin:	n/a
20	chr12:123471054-123471104	HUVEC	blood vessel:	n/a
21	chr12:123471054-123471104	GM12892	blood:	n/a
22	chr12:123471054-123471104	PANC-1	pancreas:	n/a
23	chr12:123471054-123471104	Hela-S3	cervix:	n/a
24	chr12:123471054-123471104	HCF	heart:	n/a
25	chr12:123471054-123471104	GM19239	blood:	n/a
26	chr12:123471054-123471104	HMEC	breast:	n/a
27	chr12:123471054-123471104	NHBE	bronchial:	n/a
28	chr12:123471054-123471104	BJ	skin:	n/a
29	chr12:123471054-123471104	Caco-2	colon:	n/a
30	chr12:123471054-123471104	HNPCEpiC	eye:	n/a
31	chr12:123471054-123471104	SK-N-SH	brain:	n/a
32	chr12:123471054-123471104	ProgFib	skin:	n/a
33	chr12:123471054-123471104	LNCaP	prostate:	n/a
34	chr12:123471054-123471104	PFSK-1	brain:	n/a
35	chr12:123471054-123471104	SK-N-SH_RA	brain:	n/a
36	chr12:123471054-123471104	HRE	kidney:	n/a
37	chr12:123471054-123471104	GM06990	blood:	n/a
38	chr12:123471054-123471104	HPAEpiC	pulmonary alveolar:	n/a
39	chr12:123471054-123471104	H1-hESC	embryonic stem cell:	embryo
40	chr12:123471054-123471104	ovcar-3	ovarian:	n/a
41	chr12:123471054-123471104	NHDF-neo	bronchial:	n/a
42	chr12:123471054-123471104	MCF10A-Er-Src	breast:	n/a
43	chr12:123471054-123471104	HCT-116	colon:	n/a
44	chr12:123471054-123471104	T-47D	breast:	n/a
45	chr12:123471054-123471104	Jurkat	blood:	n/a
46	chr12:123471054-123471104	NB4	blood:	n/a
47	chr12:123471054-123471104	SK-N-MC	brain:	n/a
48	chr12:123471054-123471104	AG04449	skin:	fetal
49	chr12:123471054-123471104	NT2-D1	testis:	n/a
50	chr12:123471054-123471104	AG09319	gingival:	n/a

(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	chr12:123470879..123473811-chr12:123715857..123717754,3	K562	blood:

No data

Variant related genes	Relation type
ABCB9	TF binding region
ABCB9	CpG island
ENSG00000130921	Chromatin interaction
ENSG00000090975	Chromatin interaction
ENSG00000051825	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1260294	0.80[EUR][1000 genomes]
rs12820906	0.83[EUR][1000 genomes]
rs12828755	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1463877	0.97[EUR][1000 genomes]
rs4148856	0.92[EUR][1000 genomes]
rs520088	0.88[EUR][1000 genomes]
rs585522	0.82[EUR][1000 genomes]
rs655293	0.88[EUR][1000 genomes]
rs71444568	0.87[EUR][1000 genomes]
rs883263	0.96[EUR][1000 genomes]
rs883563	0.92[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
rs12811109	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs12811109	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs12811109	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs12811109	CDK2AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs12811109	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs12811109	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs12811109	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs12811109	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 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	chr12:123466600-123471400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:123466600-123483400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:123466800-123472000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:123466800-123472400	Genic enhancers	Spleen	Spleen
7	chr12:123466800-123516000	Weak transcription	Small Intestine	intestine
8	chr12:123467000-123474000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:123467400-123472000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:123467600-123504000	Weak transcription	Hela-S3	cervix
11	chr12:123468000-123486200	Strong transcription	Fetal Brain Female	brain
12	chr12:123468200-123471400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr12:123468200-123471800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr12:123468200-123476800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:123468200-123477800	Strong transcription	Brain Germinal Matrix	brain
16	chr12:123468600-123471600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:123468800-123471400	Weak transcription	Primary B cells from cord blood	blood
18	chr12:123468800-123477000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:123468800-123485200	Weak transcription	Aorta	Aorta
20	chr12:123469000-123471800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr12:123469000-123472800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr12:123469000-123476600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:123469200-123477400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr12:123469200-123498600	Strong transcription	Primary T cells from cord blood	blood
25	chr12:123469400-123473000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:123469400-123473800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:123469400-123479400	Weak transcription	Psoas Muscle	Psoas
28	chr12:123469400-123491600	Weak transcription	HMEC	breast
29	chr12:123469400-123509400	Weak transcription	NHDF-Ad	bronchial
30	chr12:123469400-123509600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr12:123469600-123471600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr12:123469600-123473800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:123469600-123474000	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr12:123469600-123474800	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr12:123469600-123475200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr12:123469600-123475200	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr12:123469600-123475600	Strong transcription	Placenta Amnion	Placenta Amnion
38	chr12:123469600-123477000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr12:123469600-123477000	Strong transcription	Colonic Mucosa	Colon
40	chr12:123469600-123484600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr12:123469600-123493200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr12:123469800-123471200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:123469800-123471600	Weak transcription	A549	lung
44	chr12:123469800-123473000	Weak transcription	Colon Smooth Muscle	Colon
45	chr12:123469800-123473400	Weak transcription	HUVEC	blood vessel
46	chr12:123469800-123473800	Strong transcription	Fetal Intestine Large	intestine
47	chr12:123469800-123485800	Strong transcription	Placenta	Placenta
48	chr12:123469800-123486800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr12:123469800-123491400	Weak transcription	HSMMtube	muscle
50	chr12:123469800-123491600	Weak transcription	Osteobl	bone

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