Variant report

Variant	rs11172310
Chromosome Location	chr12:58116969-58116970
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:58116587-58118899	GM19193	blood:	n/a	n/a
2	NFATC1	chr12:58116681-58117019	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:58116920-58117030	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:58116495-58119415	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:58116503-58119299	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:58116328-58119086	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:58116411-58117973	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr12:58116335-58118479	GM12892	blood:	n/a	n/a
9	POLR2A	chr12:58116531-58117531	K562	blood:	n/a	n/a
10	POLR2A	chr12:58116709-58117004	GM12892	blood:	n/a	n/a
11	POLR2A	chr12:58116930-58117480	K562	blood:	n/a	n/a
12	POLR2A	chr12:58116870-58117350	HUVEC	blood vessel:	n/a	n/a
13	HA-E2F1	chr12:58116744-58117499	MCF-7	breast:	n/a	chr12:58117184-58117191
14	POLR2A	chr12:58112700-58119120	GM12891	blood:	n/a	n/a
15	POLR2A	chr12:58116535-58118789	K562	blood:	n/a	n/a
16	POLR2A	chr12:58114798-58119096	K562	blood:	n/a	n/a
17	POLR2A	chr12:58116896-58117282	U87	brain:	n/a	n/a
18	POLR2A	chr12:58116445-58118432	HL-60	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58116094..58117634-chr12:58133329..58135229,2	K562	blood:
2	chr12:57906816..57909799-chr12:58115546..58118135,2	K562	blood:
3	chr12:58085694..58088995-chr12:58116929..58123534,7	MCF-7	breast:
4	chr12:58115495..58117239-chr12:58136525..58139362,3	K562	blood:
5	chr12:58099859..58102384-chr12:58116011..58117778,2	MCF-7	breast:
6	chr12:58104338..58106820-chr12:58115614..58118088,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257342	TF binding region
AGAP2-AS1	TF binding region
ENSG00000135506	Chromatin interaction
ENSG00000135452	Chromatin interaction
ENSG00000264046	Chromatin interaction
ENSG00000166986	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11172302	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11172305	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172314	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12296750	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12307841	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12318065	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12422249	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12424011	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs184712	0.85[ASN][1000 genomes]
rs2239891	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34854770	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3893002	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760169	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	esv1851618	chr12:58109302-58131947	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv559045	chr12:58112189-58165085	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58094400-58119600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:58098400-58117600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr12:58106200-58120000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr12:58110000-58119800	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr12:58112200-58119600	Weak transcription	NHDF-Ad	bronchial
6	chr12:58113200-58117400	Weak transcription	Fetal Kidney	kidney
7	chr12:58113400-58119600	Weak transcription	Hela-S3	cervix
8	chr12:58113400-58119600	Weak transcription	HSMM	muscle
9	chr12:58113400-58119600	Weak transcription	NHEK	skin
10	chr12:58113600-58117000	Weak transcription	K562	blood
11	chr12:58113600-58119200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:58113800-58117800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:58113800-58119800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr12:58114000-58117800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:58114000-58120600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr12:58114200-58119600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr12:58114400-58119000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:58114400-58119600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr12:58114600-58117200	Weak transcription	Stomach Mucosa	stomach
20	chr12:58114800-58117600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:58115000-58119200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:58115000-58119800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr12:58115000-58120800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:58115200-58117000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:58115200-58118000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:58115200-58118200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr12:58115200-58119600	Weak transcription	HUVEC	blood vessel
28	chr12:58115200-58123600	Weak transcription	GM12878-XiMat	blood
29	chr12:58115400-58118000	Weak transcription	Osteobl	bone
30	chr12:58115400-58119000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr12:58115400-58119600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr12:58115400-58119600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr12:58115400-58119600	Weak transcription	HepG2	liver
34	chr12:58115600-58118200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr12:58115600-58119000	Weak transcription	Primary B cells from cord blood	blood
36	chr12:58115600-58119200	Weak transcription	HMEC	breast
37	chr12:58115600-58119600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr12:58115600-58119600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:58115600-58119600	Weak transcription	Colonic Mucosa	Colon
40	chr12:58115600-58119800	Weak transcription	Pancreas	Pancrea
41	chr12:58115600-58124000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr12:58115800-58117200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:58115800-58117200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:58115800-58117200	Weak transcription	A549	lung
45	chr12:58115800-58117400	Weak transcription	Fetal Lung	lung
46	chr12:58115800-58117600	Weak transcription	Fetal Intestine Large	intestine
47	chr12:58115800-58118000	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr12:58115800-58118000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr12:58115800-58118000	Weak transcription	Brain Hippocampus Middle	brain
50	chr12:58115800-58118400	Weak transcription	Primary T cells from cord blood	blood

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