Variant report

Variant	rs691114
Chromosome Location	chr19:39573918-39573919
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39573908-39574345	HCT-116	colon:	n/a	n/a
2	POLR2A	chr19:39573363-39574698	U87	brain:	n/a	n/a
3	POLR2A	chr19:39573530-39574482	U87	brain:	n/a	n/a
4	POLR2A	chr19:39573334-39574698	U87	brain:	n/a	n/a
5	POLR2A	chr19:39572561-39575566	K562	blood:	n/a	n/a
6	POLR2A	chr19:39573476-39574482	U87	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39572549..39576644-chr19:39655893..39659798,4	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC011443.1-1	chr19:39572421-39575494	expReg_chr19_5096_+

No data

Variant related genes	Relation type
ENSG00000183760	TF binding region
ENSG00000130669	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10407957	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10408661	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12151180	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2569365	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34738600	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs377373	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs380679	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs384605	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs385681	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392005	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs392135	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs393559	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs395387	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs396616	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs397189	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs400011	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs420682	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs426076	0.95[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];0.84[LWK][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs452666	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs453853	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802015	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4803196	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4803197	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs482679	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs487456	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs578940	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs597995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602744	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs609327	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs620642	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs621580	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs648192	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs648635	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs665998	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs690812	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs691059	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs691256	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs691266	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs691391	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs691890	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs692294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692343	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs692347	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs774727	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs774927	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774928	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]

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	nsv458571	chr19:39533754-39628050	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv579508	chr19:39533754-39628050	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv522530	chr19:39552150-39573918	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1067028	chr19:39567228-39622846	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1060469	chr19:39567228-39624790	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs691114	GIPR	cis	parietal	SCAN
rs691114	TGFB1	cis	parietal	SCAN
rs691114	KCNN4	cis	cerebellum	SCAN
rs691114	PSG3	cis	parietal	SCAN
rs691114	PVRL2	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39567400-39574000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:39573000-39574000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:39573000-39574200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:39573000-39575600	Flanking Active TSS	HMEC	breast
5	chr19:39573200-39574000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
6	chr19:39573200-39574000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr19:39573400-39574000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr19:39573400-39574200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
9	chr19:39573400-39574600	Flanking Active TSS	NHEK	skin
10	chr19:39573400-39574800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
11	chr19:39573400-39575000	Enhancers	A549	lung
12	chr19:39573400-39575400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr19:39573400-39575400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr19:39573400-39575600	Active TSS	Brain Substantia Nigra	brain
15	chr19:39573600-39574000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
16	chr19:39573600-39574000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr19:39573600-39574000	Enhancers	HUVEC	blood vessel
18	chr19:39573600-39574000	Flanking Active TSS	NHDF-Ad	bronchial
19	chr19:39573600-39574200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
20	chr19:39573600-39574200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
21	chr19:39573600-39574400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
22	chr19:39573600-39574400	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:39573600-39574800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
24	chr19:39573600-39574800	Enhancers	Liver	Liver
25	chr19:39573600-39575200	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr19:39573600-39575600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
27	chr19:39573800-39574000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
28	chr19:39573800-39574000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr19:39573800-39574000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr19:39573800-39574000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
31	chr19:39573800-39574000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
32	chr19:39573800-39574000	Active TSS	Brain Angular Gyrus	brain
33	chr19:39573800-39574000	Flanking Active TSS	Brain Anterior Caudate	brain
34	chr19:39573800-39574000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
35	chr19:39573800-39574000	Bivalent Enhancer	Fetal Intestine Small	intestine
36	chr19:39573800-39574000	Active TSS	Hela-S3	cervix
37	chr19:39573800-39574200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
38	chr19:39573800-39574200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr19:39573800-39574200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
40	chr19:39573800-39574200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr19:39573800-39574200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
42	chr19:39573800-39574200	Active TSS	Brain Hippocampus Middle	brain
43	chr19:39573800-39574400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
44	chr19:39573800-39574400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
45	chr19:39573800-39574400	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr19:39573800-39574400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
47	chr19:39573800-39574400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr19:39573800-39574400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
49	chr19:39573800-39574600	Bivalent Enhancer	Adipose Nuclei	Adipose
50	chr19:39573800-39574600	Flanking Active TSS	Osteobl	bone

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