Variant report

Variant	rs691391
Chromosome Location	chr19:39574722-39574723
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:39574660-39574810	HMEC	breast:	n/a	chr19:39574740-39574749
2	POLR2A	chr19:39574414-39575237	HCT-116	colon:	n/a	n/a
3	POLR2A	chr19:39574679-39574731	MCF-7	breast:	n/a	n/a
4	ELF1	chr19:39574628-39575219	MCF-7	breast:	n/a	n/a
5	MYC	chr19:39574720-39574736	MCF-7	breast:	n/a	n/a
6	POLR2A	chr19:39572561-39575566	K562	blood:	n/a	n/a
7	CTCF	chr19:39574660-39574810	SAEC	small airway:	n/a	chr19:39574740-39574749
8	GTF2F1	chr19:39574600-39574744	H1-hESC	embryonic stem cell:	n/a	n/a
9	SIN3A	chr19:39574531-39574747	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr19:39574660-39574810	Caco-2	colon:	n/a	chr19:39574740-39574749
11	POLR2A	chr19:39574398-39575208	HCT-116	colon:	n/a	n/a
12	MAX	chr19:39574549-39575249	MCF-7	breast:	n/a	chr19:39574737-39574748
13	YY1	chr19:39574557-39574776	HCT-116	colon:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:39574712-39574762	PFSK-1	brain:	n/a
2	chr19:39574712-39574762	HPAEpiC	pulmonary alveolar:	n/a
3	chr19:39574712-39574762	A549	lung:	n/a
4	chr19:39574712-39574762	HRPEpiC	eye:	n/a
5	chr19:39574712-39574762	NB4	blood:	n/a
6	chr19:39574712-39574762	HepG2	liver:	n/a
7	chr19:39574712-39574762	MCF10A-Er-Src	breast:	n/a
8	chr19:39574712-39574762	PANC-1	pancreas:	n/a
9	chr19:39574712-39574762	T-47D	breast:	n/a
10	chr19:39574712-39574762	HCM	heart:	n/a
11	chr19:39574712-39574762	ovcar-3	ovarian:	n/a
12	chr19:39574712-39574762	NT2-D1	testis:	n/a
13	chr19:39574712-39574762	HEK293	kidney:	embryo
14	chr19:39574712-39574762	AoSMC	blood vessel:	n/a
15	chr19:39574712-39574762	GM19239	blood:	n/a
16	chr19:39574712-39574762	NHBE	bronchial:	n/a
17	chr19:39574712-39574762	HRE	kidney:	n/a
18	chr19:39574712-39574762	Jurkat	blood:	n/a
19	chr19:39574712-39574762	SK-N-MC	brain:	n/a
20	chr19:39574712-39574762	HNPCEpiC	eye:	n/a
21	chr19:39574712-39574762	CMK	blood:	n/a
22	chr19:39574712-39574762	H1-hESC	embryonic stem cell:	embryo
23	chr19:39574712-39574762	NH-A	brain:	n/a
24	chr19:39574712-39574762	HUVEC	blood vessel:	n/a
25	chr19:39574712-39574762	BE2_C	brain:	n/a
26	chr19:39574712-39574762	U87	brain:	n/a
27	chr19:39574712-39574762	ECC-1	luminal epithelium:	n/a
28	chr19:39574712-39574762	HEEpiC	esophagus:	n/a
29	chr19:39574712-39574762	IMR90	lung:	fetal
30	chr19:39574712-39574762	HCPEpiC	choroid plexus:	n/a
31	chr19:39574712-39574762	AG04450	lung:	fetal
32	chr19:39574712-39574762	GM12892	blood:	n/a
33	chr19:39574712-39574762	HIPEpiC	eye:	n/a
34	chr19:39574712-39574762	HMEC	breast:	n/a
35	chr19:39574712-39574762	RPTEC	kidney:	n/a
36	chr19:39574712-39574762	GM12878	blood:	n/a
37	chr19:39574712-39574762	K562	blood:	n/a
38	chr19:39574712-39574762	ProgFib	skin:	n/a
39	chr19:39574712-39574762	PrEC	prostate:	n/a
40	chr19:39574712-39574762	AG04449	skin:	fetal
41	chr19:39574712-39574762	SKMC	muscle:	n/a
42	chr19:39574712-39574762	AG10803	skin:	n/a
43	chr19:39574712-39574762	LNCaP	prostate:	n/a
44	chr19:39574712-39574762	Hepatocyte	liver:	n/a
45	chr19:39574712-39574762	HL-60	blood:	n/a
46	chr19:39574712-39574762	SAEC	small airway:	n/a
47	chr19:39574712-39574762	AG09309	skin:	n/a
48	chr19:39574712-39574762	Caco-2	colon:	n/a
49	chr19:39574712-39574762	AG09319	gingival:	n/a
50	chr19:39574712-39574762	HCT-116	colon:	n/a

(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
ENSG00000183760	CpG island
ENSG00000130669	Chromatin interaction

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

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

rs_ID	r²[population]
rs10407957	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10408661	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12151180	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2569365	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34738600	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs377373	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs380679	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs384605	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs385681	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs392005	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs392135	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs393559	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs395387	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs396616	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs397189	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs400011	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs420682	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs426076	0.95[CEU][hapmap];0.94[CHB][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs452666	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs453853	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4802015	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4803196	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4803197	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs482679	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs487456	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs578940	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs597995	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs602744	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs609327	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs620642	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs621580	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs648192	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs648635	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs665998	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs690812	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs691059	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs691114	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]
rs691256	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs691266	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs691890	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs692294	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs692343	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs692347	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs774727	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs774927	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs774928	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
4	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
5	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
6	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

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39573000-39575600	Flanking Active TSS	HMEC	breast
2	chr19:39573400-39574800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
3	chr19:39573400-39575000	Enhancers	A549	lung
4	chr19:39573400-39575400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr19:39573400-39575400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr19:39573400-39575600	Active TSS	Brain Substantia Nigra	brain
7	chr19:39573600-39574800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
8	chr19:39573600-39574800	Enhancers	Liver	Liver
9	chr19:39573600-39575200	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr19:39573600-39575600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
11	chr19:39573800-39574800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
12	chr19:39573800-39575000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr19:39573800-39575200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
14	chr19:39573800-39575400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr19:39573800-39575400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr19:39574000-39574800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
17	chr19:39574000-39574800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
18	chr19:39574000-39575200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
19	chr19:39574000-39575400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
20	chr19:39574000-39575400	Flanking Active TSS	HUVEC	blood vessel
21	chr19:39574000-39575400	Active TSS	NHDF-Ad	bronchial
22	chr19:39574200-39574800	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
23	chr19:39574200-39574800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
24	chr19:39574200-39574800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
25	chr19:39574200-39574800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
26	chr19:39574200-39574800	Bivalent Enhancer	Stomach Mucosa	stomach
27	chr19:39574200-39575000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:39574200-39575200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
29	chr19:39574200-39575200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr19:39574200-39575400	Active TSS	H9 Cell Line	embryonic stem cell
31	chr19:39574200-39575400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr19:39574200-39575600	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr19:39574200-39576400	Weak transcription	Right Atrium	heart
34	chr19:39574400-39574800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr19:39574400-39574800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr19:39574400-39574800	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 1	blood
37	chr19:39574400-39574800	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
38	chr19:39574400-39574800	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
39	chr19:39574400-39574800	Flanking Bivalent TSS/Enh	Placenta	Placenta
40	chr19:39574400-39574800	Enhancers	Right Ventricle	heart
41	chr19:39574400-39575000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
42	chr19:39574400-39575200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr19:39574400-39575200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
44	chr19:39574400-39575200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
45	chr19:39574400-39575200	Bivalent Enhancer	Fetal Muscle Leg	muscle
46	chr19:39574400-39575200	Enhancers	Pancreas	Pancrea
47	chr19:39574400-39575400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr19:39574400-39575400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
49	chr19:39574400-39575400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
50	chr19:39574400-39575400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell

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