Variant report

Variant	rs55742290
Chromosome Location	chr12:123466111-123466112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:123462700-123467376	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:123464394-123466358	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr12:123465981-123466325	MCF-7	breast:	n/a	n/a
4	POLR2A	chr12:123458534-123466263	K562	blood:	n/a	n/a
5	ZNF263	chr12:123465724-123466694	HEK293-T-REx	kidney:	n/a	chr12:123466218-123466239
6	POLR2A	chr12:123462020-123470019	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr12:123464066-123466242	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr12:123464276-123466236	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr12:123464006-123466178	GM12878	blood:	n/a	n/a
10	UBTF	chr12:123464802-123466120	K562	blood:	n/a	n/a
11	POLR2A	chr12:123464088-123466135	Raji	blood:	n/a	n/a
12	NR2F2	chr12:123465286-123466239	K562	blood:	n/a	n/a
13	POLR2A	chr12:123463985-123466171	U87	brain:	n/a	n/a
14	UBTF	chr12:123464683-123466295	K562	blood:	n/a	n/a
15	POLR2A	chr12:123463863-123469964	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr12:123463573-123466152	GM12892	blood:	n/a	n/a
17	POLR2A	chr12:123463985-123466477	U87	brain:	n/a	n/a
18	STAT5A	chr12:123465848-123466200	GM12878	blood:	n/a	n/a
19	POLR2A	chr12:123462777-123467143	HL-60	blood:	n/a	n/a
20	POLR2A	chr12:123464136-123466124	GM19193	blood:	n/a	n/a
21	POLR2A	chr12:123463577-123466137	GM12878	blood:	n/a	n/a
22	SIN3AK20	chr12:123464491-123466183	MCF-7	breast:	n/a	n/a
23	POLR2A	chr12:123465883-123466428	PANC-1	pancreas:	n/a	n/a
24	POLR2A	chr12:123464755-123466116	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr12:123463126-123466154	GM12878	blood:	n/a	n/a
26	POLR2A	chr12:123463370-123466657	PFSK-1	brain:	n/a	n/a
27	MTA3	chr12:123464061-123466131	GM12878	blood:	n/a	n/a
28	POLR2A	chr12:123461706-123470094	K562	blood:	n/a	n/a
29	POLR2A	chr12:123465726-123466143	GM12878	blood:	n/a	n/a
30	MXI1	chr12:123464266-123466223	IMR90	lung:	n/a	n/a
31	YY1	chr12:123464569-123466137	SK-N-SH	brain:	n/a	chr12:123464818-123464832
32	POLR2A	chr12:123462647-123470505	Hela-S3	cervix:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123464088..123467689-chr12:123493302..123498202,6	MCF-7	breast:
2	chr12:123343068..123345101-chr12:123464542..123466196,2	MCF-7	breast:
3	chr12:123463846..123466792-chr12:123754381..123757110,2	MCF-7	breast:
4	chr12:123463900..123467066-chr12:123633750..123636695,4	K562	blood:
5	chr12:123465466..123466394-chr16:18812294..18813236,3	Hela-S3	cervix:
6	chr12:123341647..123346113-chr12:123465146..123467618,4	K562	blood:
7	chr12:123317692..123320507-chr12:123463597..123466562,3	MCF-7	breast:
8	chr12:123345343..123346928-chr12:123463907..123466458,2	MCF-7	breast:
9	chr12:122710527..122712234-chr12:123464292..123467088,2	K562	blood:
10	chr12:123463210..123468211-chr12:123716151..123721062,7	MCF-7	breast:
11	chr12:123465824..123467766-chr12:123717384..123719608,2	MCF-7	breast:
12	chr12:123349459..123352177-chr12:123465556..123468107,2	K562	blood:
13	chr12:123318837..123320791-chr12:123463752..123466824,3	MCF-7	breast:
14	chr12:123465881..123468570-chr12:123716034..123719414,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OGFOD2-1	chr12:123465676-123466426	NONHSAT031551

No data

Variant related genes	Relation type
ARL6IP4	TF binding region
ENSG00000265526	Chromatin interaction
ENSG00000090975	Chromatin interaction
ENSG00000184047	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000256152	Chromatin interaction
ENSG00000170540	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000260342	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10773921	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11608811	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11613937	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12425009	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12425850	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1984658	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28755851	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3741530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3759115	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3897102	0.91[ASN][1000 genomes]
rs4275659	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61955196	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61955214	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7135296	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7296418	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7305511	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7957096	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs883562	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs884956	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

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
rs55742290	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs55742290	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs55742290	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs55742290	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs55742290	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs55742290	SBNO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 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	chr12:123463800-123466400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:123464000-123466600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr12:123464000-123466800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:123464200-123466400	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr12:123464400-123466200	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr12:123464400-123466200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:123464400-123466400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:123464400-123466400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:123464400-123466400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:123464400-123466400	Active TSS	Fetal Kidney	kidney
12	chr12:123464600-123466200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:123464600-123466200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:123464600-123466200	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr12:123464600-123466200	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr12:123464600-123466200	Active TSS	Aorta	Aorta
17	chr12:123464600-123466200	Active TSS	Fetal Intestine Large	intestine
18	chr12:123464600-123466200	Active TSS	Ovary	ovary
19	chr12:123464600-123466200	Active TSS	Placenta Amnion	Placenta Amnion
20	chr12:123464600-123466200	Active TSS	Sigmoid Colon	Sigmoid Colon
21	chr12:123464600-123466200	Active TSS	Small Intestine	intestine
22	chr12:123464600-123466200	Active TSS	NHDF-Ad	bronchial
23	chr12:123464600-123466200	Active TSS	NHLF	lung
24	chr12:123464600-123466800	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr12:123464600-123467000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:123464800-123466200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:123464800-123466200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:123464800-123466200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:123464800-123466200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr12:123464800-123466200	Active TSS	Muscle Satellite Cultured Cells	--
31	chr12:123464800-123466200	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr12:123464800-123466200	Active TSS	Gastric	stomach
33	chr12:123464800-123466200	Active TSS	GM12878-XiMat	blood
34	chr12:123464800-123466200	Bivalent/Poised TSS	HepG2	liver
35	chr12:123464800-123466200	Active TSS	HSMM	muscle
36	chr12:123464800-123466200	Active TSS	HSMMtube	muscle
37	chr12:123464800-123466200	Active TSS	HUVEC	blood vessel
38	chr12:123464800-123466200	Active TSS	NH-A	brain
39	chr12:123464800-123466400	Active TSS	H1 Cell Line	embryonic stem cell
40	chr12:123464800-123466400	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr12:123464800-123466400	Active TSS	A549	lung
42	chr12:123465000-123466200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:123465000-123466200	Active TSS	Brain Substantia Nigra	brain
44	chr12:123465000-123466200	Active TSS	Fetal Thymus	thymus
45	chr12:123465000-123466200	Active TSS	HMEC	breast
46	chr12:123465000-123466200	Active TSS	NHEK	skin
47	chr12:123465400-123466200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
48	chr12:123465400-123466800	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr12:123465600-123466200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:123465600-123466200	Flanking Active TSS	Placenta	Placenta

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