Variant report

Variant	rs12976749
Chromosome Location	chr19:39119494-39119495
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	chr19:39114094-39125094	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:39119344-39121063	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr19:39119423-39119672	K562	blood:	n/a	n/a
4	POLR2A	chr19:39119365-39119506	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39106830..39111691-chr19:39117375..39123240,7	MCF-7	breast:
2	chr19:39118492..39120999-chr19:39123202..39126576,3	MCF-7	breast:

Variant related genes	Relation type
EIF3K	TF binding region
ENSG00000104814	Chromatin interaction
ENSG00000178982	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12462503	0.81[CHB][hapmap]
rs12977469	0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.91[ASN][1000 genomes]
rs12984247	0.81[CHB][hapmap]
rs1862371	0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs3786834	0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6508813	0.81[CHB][hapmap]
rs752067	0.81[CHB][hapmap]
rs888994	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.96[ASN][1000 genomes]
rs9304576	0.86[CHB][hapmap]
rs9304577	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	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
7	nsv1057901	chr19:39112486-39174332	Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12976749	GIPR	cis	parietal	SCAN
rs12976749	ATP1A3	cis	parietal	SCAN
rs12976749	CYP2F1	cis	cerebellum	SCAN
rs12976749	CAPN12	Cis_1M	lymphoblastoid	RTeQTL
rs12976749	TMEM145	cis	parietal	SCAN
rs12976749	SELV	cis	parietal	SCAN
rs12976749	MEGF8	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39110400-39122600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39110800-39120800	Strong transcription	H9 Cell Line	embryonic stem cell
3	chr19:39110800-39120800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:39111000-39121000	Strong transcription	Ovary	ovary
5	chr19:39111000-39121600	Strong transcription	Fetal Intestine Large	intestine
6	chr19:39111000-39122600	Strong transcription	Fetal Intestine Small	intestine
7	chr19:39111000-39124000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr19:39111000-39124400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr19:39111000-39124600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr19:39111000-39125000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:39111000-39127000	Strong transcription	Thymus	Thymus
12	chr19:39111000-39127400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr19:39111000-39128800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr19:39111200-39120600	Strong transcription	HMEC	breast
15	chr19:39111200-39120800	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr19:39111200-39120800	Strong transcription	Gastric	stomach
17	chr19:39111200-39120800	Strong transcription	HUVEC	blood vessel
18	chr19:39111200-39121000	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr19:39111200-39121400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:39111200-39121400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr19:39111200-39121600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr19:39111200-39121600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr19:39111200-39121600	Strong transcription	Right Ventricle	heart
24	chr19:39111200-39121800	Strong transcription	Brain Cingulate Gyrus	brain
25	chr19:39111200-39121800	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr19:39111200-39122200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr19:39111200-39122400	Strong transcription	Colonic Mucosa	Colon
28	chr19:39111200-39123600	Strong transcription	Osteobl	bone
29	chr19:39111200-39123800	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr19:39111200-39123800	Strong transcription	Primary B cells from peripheral blood	blood
31	chr19:39111200-39123800	Strong transcription	Primary T cells from cord blood	blood
32	chr19:39111200-39124000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:39111200-39124000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr19:39111200-39124000	Strong transcription	Liver	Liver
35	chr19:39111200-39124000	Strong transcription	Brain Angular Gyrus	brain
36	chr19:39111200-39124000	Strong transcription	Placenta	Placenta
37	chr19:39111200-39124000	Strong transcription	Fetal Thymus	thymus
38	chr19:39111200-39124000	Strong transcription	Left Ventricle	heart
39	chr19:39111200-39124000	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr19:39111200-39124200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:39111200-39124200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr19:39111200-39124200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr19:39111200-39124200	Strong transcription	Brain Germinal Matrix	brain
44	chr19:39111200-39124200	Strong transcription	Fetal Brain Female	brain
45	chr19:39111200-39124200	Strong transcription	Lung	lung
46	chr19:39111200-39124400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr19:39111200-39124400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr19:39111200-39124400	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr19:39111200-39124400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr19:39111200-39124400	Strong transcription	Adipose Nuclei	Adipose

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