Variant report

Variant	rs12319666
Chromosome Location	chr12:57624781-57624782
allele	G/T
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	chr12:57622967-57627887	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:57622661-57625191	U87	brain:	n/a	n/a
3	POLR2A	chr12:57622952-57624837	GM12892	blood:	n/a	n/a
4	POLR2A	chr12:57622811-57628074	HepG2	liver:	n/a	n/a
5	MXI1	chr12:57622692-57624810	IMR90	lung:	n/a	chr12:57623211-57623226
6	POLR2A	chr12:57623360-57624827	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:57622648-57625404	PFSK-1	brain:	n/a	n/a
8	SREBP1	chr12:57624416-57628801	HepG2	liver:	n/a	chr12:57627314-57627325
9	STAT5A	chr12:57623294-57624804	GM12878	blood:	n/a	chr12:57624573-57624581
10	POLR2A	chr12:57622693-57625205	U87	brain:	n/a	n/a
11	MXI1	chr12:57622776-57624827	SK-N-SH	brain:	n/a	chr12:57623211-57623226
12	POLR2A	chr12:57624331-57624902	U87	brain:	n/a	n/a
13	POLR2A	chr12:57622758-57624862	SK-N-MC	brain:	n/a	n/a
14	HEY1	chr12:57623217-57625003	HepG2	liver:	n/a	n/a
15	POLR2A	chr12:57624621-57624911	GM12878	blood:	n/a	n/a
16	ZNF263	chr12:57623482-57626590	HEK293-T-REx	kidney:	n/a	chr12:57626413-57626422 chr12:57625025-57625034
17	POLR2A	chr12:57622980-57624922	MCF10A-Er-Src	breast:	n/a	n/a
18	MAX	chr12:57623166-57624807	A549	lung:	n/a	chr12:57623696-57623703
19	POLR2A	chr12:57623235-57624830	ECC-1	luminal epithelium:	n/a	n/a
20	MTA3	chr12:57623290-57624793	GM12878	blood:	n/a	n/a
21	POLR2A	chr12:57624668-57624911	K562	blood:	n/a	n/a
22	POLR2A	chr12:57623319-57624842	GM18505	blood:	n/a	n/a
23	POLR2A	chr12:57623260-57624882	HL-60	blood:	n/a	n/a
24	CTCF	chr12:57624566-57624828	T-47D	breast:	n/a	n/a
25	POLR2A	chr12:57622485-57625200	PFSK-1	brain:	n/a	n/a
26	POLR2A	chr12:57623320-57624814	GM12878	blood:	n/a	n/a
27	POLR2A	chr12:57624432-57624834	K562	blood:	n/a	n/a
28	POLR2A	chr12:57624461-57624817	MCF-7	breast:	n/a	n/a
29	RELA	chr12:57622802-57624934	GM18951	blood:	n/a	n/a
30	POLR2A	chr12:57622615-57625235	IMR90	lung:	n/a	n/a
31	POLR2A	chr12:57623308-57633262	Hela-S3	cervix:	n/a	n/a
32	HCFC1	chr12:57622313-57625003	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr12:57623302-57624824	HepG2	liver:	n/a	n/a
34	POLR2A	chr12:57623200-57624833	GM12878	blood:	n/a	n/a
35	POLR2A	chr12:57624286-57624847	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57482485..57484872-chr12:57623536..57625179,2	MCF-7	breast:
2	chr12:57480219..57483297-chr12:57622863..57624907,4	MCF-7	breast:
3	chr12:57622307..57625065-chr12:57914079..57916302,2	K562	blood:
4	chr12:57472467..57474129-chr12:57624137..57625986,2	K562	blood:

Variant related genes	Relation type
SHMT2	TF binding region
ENSG00000166987	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000166886	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12312567	1.00[MEX][hapmap]
rs12369946	1.00[MEX][hapmap]
rs2229277	1.00[MEX][hapmap]
rs35835063	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv518980	chr12:57532982-57637593	Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv1810281	chr12:57558657-57641094	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	esv1827238	chr12:57561918-57641094	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv1796377	chr12:57577246-57638936	Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	esv1809338	chr12:57580227-57628338	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv1827692	chr12:57582852-57651345	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv519293	chr12:57583672-57637593	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57622600-57624800	Active TSS	HSMMtube	muscle
2	chr12:57622800-57624800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
3	chr12:57622800-57625000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:57623000-57624800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
5	chr12:57623000-57624800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
6	chr12:57623000-57624800	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr12:57623000-57624800	Flanking Active TSS	Brain Hippocampus Middle	brain
8	chr12:57623000-57624800	Flanking Active TSS	Fetal Muscle Leg	muscle
9	chr12:57623000-57624800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr12:57623200-57624800	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr12:57623200-57624800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:57623200-57624800	Flanking Active TSS	Colonic Mucosa	Colon
13	chr12:57623400-57624800	Active TSS	Aorta	Aorta
14	chr12:57623400-57624800	Flanking Active TSS	Placenta	Placenta
15	chr12:57623600-57624800	Flanking Active TSS	Fetal Muscle Trunk	muscle
16	chr12:57623600-57624800	Flanking Active TSS	Right Ventricle	heart
17	chr12:57623600-57624800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr12:57623600-57625200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
19	chr12:57623800-57624800	Flanking Active TSS	Brain Anterior Caudate	brain
20	chr12:57623800-57624800	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr12:57623800-57624800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
22	chr12:57623800-57624800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:57623800-57624800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr12:57623800-57624800	Flanking Active TSS	Fetal Brain Female	brain
25	chr12:57623800-57624800	Flanking Active TSS	Left Ventricle	heart
26	chr12:57623800-57624800	Flanking Active TSS	Lung	lung
27	chr12:57623800-57624800	Flanking Active TSS	Pancreas	Pancrea
28	chr12:57623800-57624800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
29	chr12:57623800-57624800	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
30	chr12:57623800-57625000	Flanking Active TSS	Duodenum Mucosa	Duodenum
31	chr12:57623800-57628200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:57624000-57624800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:57624000-57624800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:57624000-57624800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:57624000-57624800	Flanking Active TSS	Primary B cells from peripheral blood	blood
36	chr12:57624000-57624800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:57624000-57624800	Flanking Active TSS	Brain Angular Gyrus	brain
38	chr12:57624000-57624800	Flanking Active TSS	Brain Cingulate Gyrus	brain
39	chr12:57624000-57624800	Flanking Active TSS	Brain Substantia Nigra	brain
40	chr12:57624000-57624800	Flanking Active TSS	Fetal Lung	lung
41	chr12:57624000-57624800	Flanking Active TSS	Gastric	stomach
42	chr12:57624000-57625000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:57624000-57625000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr12:57624000-57625000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:57624000-57625200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr12:57624000-57625200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:57624000-57625200	Flanking Active TSS	HUVEC	blood vessel
48	chr12:57624000-57625400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
49	chr12:57624000-57625800	Transcr. at gene 5' and 3'	NHEK	skin
50	chr12:57624200-57624800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell

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