Variant report

Variant	rs12306711
Chromosome Location	chr12:123568186-123568187
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr12:123568161-123568566	GM12878	blood:	n/a	n/a
2	MTA3	chr12:123567879-123569132	GM12878	blood:	n/a	n/a
3	MEF2C	chr12:123568075-123568932	GM12878	blood:	n/a	n/a
4	SPI1	chr12:123567909-123568688	GM12878	blood:	n/a	n/a
5	MEF2A	chr12:123568140-123568635	GM12878	blood:	n/a	n/a
6	ELF1	chr12:123567956-123568754	GM12878	blood:	n/a	n/a
7	SPI1	chr12:123568145-123568625	GM12891	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123559703..123562585-chr12:123566918..123569407,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARL6IP4-1	chr12:123567782-123568676	ENSG00000251497
2	lnc-ARL6IP4-1	chr12:123568171-123568369	NONHSAT031564

No data

Variant related genes	Relation type
PITPNM2	TF binding region
ENSG00000090975	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10219462	0.87[ASN][1000 genomes]
rs1026395	1.00[JPT][hapmap]
rs1037593	1.00[JPT][hapmap]
rs10431343	1.00[CHB][hapmap]
rs10846468	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10846469	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846471	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10846473	1.00[ASN][1000 genomes]
rs10846484	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10848148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10848291	0.91[AMR][1000 genomes]
rs10848363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10848365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10848429	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057172	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057175	0.82[AMR][1000 genomes]
rs11057180	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs11060888	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11060932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11060997	0.87[ASN][1000 genomes]
rs11060999	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11061166	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11061589	1.00[AMR][1000 genomes]
rs11061601	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11061611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061614	0.82[AMR][1000 genomes]
rs11061616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12229119	0.87[ASN][1000 genomes]
rs12229884	0.87[ASN][1000 genomes]
rs12298355	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12302120	0.87[ASN][1000 genomes]
rs12302334	1.00[CHD][hapmap];0.91[AMR][1000 genomes]
rs12311043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12311134	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12318389	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12318594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12319324	0.82[AMR][1000 genomes]
rs12366787	1.00[ASN][1000 genomes]
rs2343107	1.00[JPT][hapmap]
rs57310784	0.87[ASN][1000 genomes]
rs59002329	0.87[ASN][1000 genomes]
rs73408859	0.87[ASN][1000 genomes]
rs73408862	0.87[ASN][1000 genomes]
rs73408863	0.87[ASN][1000 genomes]

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	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	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
3	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
4	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
5	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
6	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
7	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
8	nsv1042550	chr12:123532028-123659500	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123560200-123570400	Weak transcription	Aorta	Aorta
2	chr12:123560600-123574200	Weak transcription	Gastric	stomach
3	chr12:123561000-123578800	Weak transcription	Fetal Intestine Large	intestine
4	chr12:123561200-123590000	Weak transcription	Fetal Intestine Small	intestine
5	chr12:123561400-123568400	Weak transcription	HSMMtube	muscle
6	chr12:123561600-123568200	Weak transcription	NHEK	skin
7	chr12:123561600-123569800	Weak transcription	HSMM	muscle
8	chr12:123561600-123604000	Genic enhancers	Fetal Thymus	thymus
9	chr12:123562000-123568400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:123562000-123568800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:123562000-123569000	Weak transcription	HepG2	liver
12	chr12:123562000-123569400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:123562000-123576200	Weak transcription	Primary T cells from cord blood	blood
14	chr12:123562200-123568200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:123562200-123572600	Weak transcription	K562	blood
16	chr12:123562400-123568400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:123562400-123586600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr12:123562600-123568200	Weak transcription	Placenta	Placenta
19	chr12:123562600-123568400	Weak transcription	Brain Substantia Nigra	brain
20	chr12:123563200-123568200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:123563400-123568200	Weak transcription	Brain Anterior Caudate	brain
22	chr12:123563400-123568200	Weak transcription	Fetal Stomach	stomach
23	chr12:123563600-123568200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:123563600-123570200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr12:123563800-123568200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:123563800-123568200	Weak transcription	Brain Angular Gyrus	brain
27	chr12:123563800-123568200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr12:123563800-123568400	Weak transcription	Brain Hippocampus Middle	brain
29	chr12:123563800-123568400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:123565000-123568400	Enhancers	Primary B cells from peripheral blood	blood
31	chr12:123565000-123571400	Enhancers	Fetal Heart	heart
32	chr12:123565000-123571800	Enhancers	Right Ventricle	heart
33	chr12:123565400-123568400	Enhancers	Primary B cells from cord blood	blood
34	chr12:123565600-123571000	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr12:123566400-123570200	Enhancers	HMEC	breast
36	chr12:123566400-123571600	Enhancers	Right Atrium	heart
37	chr12:123566400-123572000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:123566600-123568200	Enhancers	Hela-S3	cervix
39	chr12:123566600-123568600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:123566600-123569000	Enhancers	Spleen	Spleen
41	chr12:123566600-123571600	Enhancers	Lung	lung
42	chr12:123566800-123568400	Weak transcription	Fetal Brain Male	brain
43	chr12:123566800-123568600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr12:123566800-123568800	Weak transcription	Fetal Brain Female	brain
45	chr12:123566800-123569600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:123567000-123568800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr12:123567200-123568400	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr12:123567200-123569400	Genic enhancers	Thymus	Thymus
49	chr12:123567200-123570200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:123567200-123570800	Enhancers	Liver	Liver

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