Variant report

Variant	rs2239891
Chromosome Location	chr12:58112437-58112438
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:58112060-58112457	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:58109324..58110865-chr12:58112345..58113937,2	K562	blood:
2	chr12:58112144..58113790-chr12:58117146..58119101,2	K562	blood:
3	chr12:58111124..58113392-chr12:58119028..58121695,2	K562	blood:

Variant related genes	Relation type
OS9	TF binding region
ENSG00000257499	Chromatin interaction
ENSG00000255737	Chromatin interaction
ENSG00000135506	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];0.97[ASN][1000 genomes]
rs11172305	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172310	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172314	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12296750	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12307841	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12318065	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12422249	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12424011	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs184712	0.82[ASN][1000 genomes]
rs34854770	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3893002	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4760169	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58089200-58115400	Weak transcription	Fetal Heart	heart
2	chr12:58091200-58116600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr12:58093400-58115400	Weak transcription	Fetal Brain Male	brain
4	chr12:58094400-58119600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:58097200-58116200	Weak transcription	Psoas Muscle	Psoas
6	chr12:58098000-58113000	Weak transcription	K562	blood
7	chr12:58098000-58115600	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr12:58098000-58115800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr12:58098000-58116000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:58098400-58115800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr12:58098400-58116000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:58098400-58117600	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr12:58098800-58116000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:58103400-58113000	Weak transcription	Hela-S3	cervix
15	chr12:58103400-58115800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:58103400-58116400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr12:58103800-58115800	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr12:58104400-58115800	Strong transcription	Duodenum Mucosa	Duodenum
19	chr12:58104800-58115400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr12:58104800-58115800	Strong transcription	Fetal Intestine Large	intestine
21	chr12:58104800-58116000	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:58105200-58116000	Strong transcription	Fetal Muscle Trunk	muscle
23	chr12:58105400-58115600	Strong transcription	Primary hematopoietic stem cells	blood
24	chr12:58105400-58116200	Strong transcription	Fetal Muscle Leg	muscle
25	chr12:58105600-58115800	Strong transcription	Primary T cells from cord blood	blood
26	chr12:58105600-58115800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:58105600-58116000	Strong transcription	Adipose Nuclei	Adipose
28	chr12:58105600-58116000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr12:58105600-58116200	Strong transcription	Fetal Stomach	stomach
30	chr12:58106000-58116000	Strong transcription	Fetal Brain Female	brain
31	chr12:58106000-58116000	Strong transcription	Thymus	Thymus
32	chr12:58106200-58116000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:58106200-58116000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr12:58106200-58116800	Strong transcription	Fetal Intestine Small	intestine
35	chr12:58106200-58120000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr12:58106400-58115400	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr12:58106400-58116000	Strong transcription	Ovary	ovary
38	chr12:58106600-58115200	Strong transcription	GM12878-XiMat	blood
39	chr12:58106600-58116000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:58106600-58116000	Strong transcription	Lung	lung
41	chr12:58106600-58116200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:58106800-58116600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr12:58107000-58116000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr12:58107200-58115800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:58107600-58115600	Strong transcription	Pancreas	Pancrea
46	chr12:58108000-58113800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr12:58108000-58116000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:58108000-58116200	Strong transcription	Brain Germinal Matrix	brain
49	chr12:58108000-58116800	Strong transcription	Spleen	Spleen
50	chr12:58108200-58113400	Strong transcription	HSMM	muscle

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