Variant report

Variant	rs12979755
Chromosome Location	chr19:39391817-39391818
allele	C/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	GATA2	chr19:39391502-39391910	HUVEC	blood vessel:	n/a	n/a
2	CEBPB	chr19:39391510-39391882	K562	blood:	n/a	chr19:39391678-39391689
3	CEBPB	chr19:39391561-39391868	IMR90	lung:	n/a	chr19:39391678-39391689
4	HCFC1	chr19:39389667-39391967	Hela-S3	cervix:	n/a	n/a
5	GATA3	chr19:39391205-39391873	SH-SY5Y	brain:	n/a	chr19:39391697-39391705
6	CEBPB	chr19:39391561-39391867	A549	lung:	n/a	chr19:39391678-39391689
7	CEBPB	chr19:39391532-39391856	K562	blood:	n/a	chr19:39391678-39391689
8	JUN	chr19:39389766-39391981	K562	blood:	n/a	chr19:39390500-39390509 chr19:39391294-39391306
9	CUX1	chr19:39390999-39391863	K562	blood:	n/a	n/a
10	CEBPB	chr19:39391563-39391879	Hela-S3	cervix:	n/a	chr19:39391678-39391689
11	SREBP1	chr19:39389738-39391854	GM12878	blood:	n/a	n/a
12	CEBPB	chr19:39391628-39391872	HepG2	liver:	n/a	chr19:39391678-39391689
13	GATA1	chr19:39389861-39391860	PBDE	blood:	n/a	chr19:39390295-39390304
14	FOXA1	chr19:39391253-39391870	HepG2	liver:	n/a	n/a
15	GATA2	chr19:39391668-39391857	SH-SY5Y	brain:	n/a	n/a
16	CEBPB	chr19:39391727-39391847	HepG2	liver:	n/a	n/a
17	GATA3	chr19:39389595-39391907	A549	lung:	n/a	chr19:39389669-39389679 chr19:39391697-39391705 chr19:39390295-39390304
18	FOXA2	chr19:39391650-39391843	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39338733..39343337-chr19:39388774..39392675,12	K562	blood:
2	chr19:39390700..39392797-chr19:39401919..39404314,3	K562	blood:
3	chr19:39320984..39323718-chr19:39390338..39392657,3	K562	blood:
4	chr19:39388836..39392687-chr19:39409083..39412619,5	K562	blood:
5	chr19:39390131..39392480-chr19:39402477..39404053,2	MCF-7	breast:
6	chr19:39388885..39392214-chr19:39419332..39422757,5	MCF-7	breast:
7	chr19:39386472..39392494-chr19:39418718..39424791,9	K562	blood:
8	chr19:39389410..39392783-chr19:39420988..39423307,4	MCF-7	breast:
9	chr19:39338023..39344706-chr19:39388476..39392998,12	MCF-7	breast:
10	chr19:39391259..39393276-chr19:39393440..39395044,2	MCF-7	breast:
11	chr19:39390485..39392144-chr19:39409724..39411734,2	MCF-7	breast:
12	chr19:39338478..39344219-chr19:39387112..39393304,19	K562	blood:

Variant related genes	Relation type
SIRT2	TF binding region
ENSG00000104824	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000262484	Chromatin interaction
ENSG00000128626	Chromatin interaction
ENSG00000104823	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10410544	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs10416055	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs10426382	1.00[JPT][hapmap]
rs10775533	0.92[ASN][1000 genomes]
rs11083485	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11083489	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11668245	0.92[ASN][1000 genomes]
rs11879872	0.86[YRI][hapmap]
rs12462710	0.92[ASN][1000 genomes]
rs12610409	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12972925	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12972986	0.92[ASN][1000 genomes]
rs17545254	0.92[ASN][1000 genomes]
rs1808662	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1865047	0.85[ASN][1000 genomes]
rs2278412	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs3136640	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801960	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4801971	0.92[ASN][1000 genomes]
rs4802998	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803006	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803034	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs575	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6508814	1.00[JPT][hapmap]
rs7257007	0.92[ASN][1000 genomes]
rs730078	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7508411	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7508539	0.92[ASN][1000 genomes]
rs8113389	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs9636109	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9749516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	esv1798153	chr19:39338663-39399277	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv911674	chr19:39391547-39398631	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12979755	SIRT2	cis	multi-tissue	Pritchard
rs12979755	MYPOP	cis	parietal	SCAN
rs12979755	LGALS14	cis	parietal	SCAN
rs12979755	ZNF285	cis	cerebellum	SCAN
rs12979755	NFKBIB	cis	multi-tissue	Pritchard
rs12979755	SARS2	cis	lymphoblastoid	seeQTL
rs12979755	PRR19	cis	parietal	SCAN
rs12979755	PLD3	cis	parietal	SCAN
rs12979755	GPR4	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39389800-39392000	Active TSS	NHEK	skin
2	chr19:39391000-39392000	Flanking Active TSS	HUVEC	blood vessel
3	chr19:39391000-39394800	Weak transcription	Spleen	Spleen
4	chr19:39391000-39395000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr19:39391000-39395800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr19:39391200-39392000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:39391200-39392000	Flanking Active TSS	Liver	Liver
8	chr19:39391200-39392000	Weak transcription	Left Ventricle	heart
9	chr19:39391200-39392000	Weak transcription	Lung	lung
10	chr19:39391200-39392200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:39391200-39392200	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr19:39391200-39392200	Enhancers	Primary B cells from peripheral blood	blood
13	chr19:39391200-39392400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr19:39391200-39392400	Flanking Active TSS	Dnd41	blood
15	chr19:39391200-39392600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr19:39391200-39392600	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr19:39391200-39394800	Weak transcription	Gastric	stomach
18	chr19:39391200-39395000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr19:39391200-39395200	Weak transcription	Pancreas	Pancrea
20	chr19:39391200-39395400	Weak transcription	Aorta	Aorta
21	chr19:39391200-39395400	Weak transcription	Esophagus	oesophagus
22	chr19:39391200-39395600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr19:39391200-39420800	Weak transcription	Small Intestine	intestine
24	chr19:39391400-39392000	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr19:39391400-39392000	Weak transcription	Fetal Stomach	stomach
26	chr19:39391400-39392200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr19:39391400-39392200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr19:39391400-39392200	Enhancers	Brain Hippocampus Middle	brain
29	chr19:39391400-39392200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr19:39391400-39392400	Enhancers	Primary T cells fromperipheralblood	blood
31	chr19:39391400-39392400	Flanking Active TSS	Hela-S3	cervix
32	chr19:39391400-39392600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr19:39391400-39392600	Enhancers	Placenta	Placenta
34	chr19:39391400-39392600	Enhancers	Stomach Mucosa	stomach
35	chr19:39391400-39395200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr19:39391400-39395600	Weak transcription	Brain Germinal Matrix	brain
37	chr19:39391400-39397400	Weak transcription	Fetal Brain Female	brain
38	chr19:39391400-39397600	Weak transcription	Psoas Muscle	Psoas
39	chr19:39391400-39402200	Weak transcription	Fetal Brain Male	brain
40	chr19:39391600-39392000	Enhancers	Primary hematopoietic stem cells	blood
41	chr19:39391600-39392200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:39391600-39392200	Enhancers	Primary B cells from cord blood	blood
43	chr19:39391600-39392200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr19:39391600-39392200	Enhancers	Fetal Intestine Small	intestine
45	chr19:39391600-39392200	Weak transcription	Fetal Thymus	thymus
46	chr19:39391600-39392400	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr19:39391600-39392400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr19:39391600-39394800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr19:39391600-39395000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr19:39391600-39395000	Weak transcription	NHDF-Ad	bronchial

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