Variant report

Variant	rs774727
Chromosome Location	chr19:39575037-39575038
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr19:39575007-39575299	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:39574414-39575237	HCT-116	colon:	n/a	n/a
3	ELF1	chr19:39574819-39575116	K562	blood:	n/a	n/a
4	ELF1	chr19:39574628-39575219	MCF-7	breast:	n/a	n/a
5	TEAD4	chr19:39575019-39575544	H1-hESC	embryonic stem cell:	n/a	n/a
6	E2F6	chr19:39574838-39575340	H1-hESC	embryonic stem cell:	n/a	chr19:39574999-39575011 chr19:39575127-39575134 chr19:39575025-39575035 chr19:39575127-39575134 chr19:39575127-39575134 chr19:39575022-39575032 chr19:39575123-39575135
7	POLR2A	chr19:39572561-39575566	K562	blood:	n/a	n/a
8	POLR2A	chr19:39574801-39575939	U87	brain:	n/a	n/a
9	POLR2A	chr19:39574879-39575236	U87	brain:	n/a	n/a
10	POLR2A	chr19:39574937-39575225	MCF-7	breast:	n/a	n/a
11	POLR2A	chr19:39574807-39575922	U87	brain:	n/a	n/a
12	REST	chr19:39574846-39575692	H1-neurons	neurons:	n/a	n/a
13	POLR2A	chr19:39574398-39575208	HCT-116	colon:	n/a	n/a
14	MAX	chr19:39574549-39575249	MCF-7	breast:	n/a	chr19:39574737-39574748
15	TBP	chr19:39574976-39575118	H1-hESC	embryonic stem cell:	n/a	n/a
16	E2F6	chr19:39574827-39575430	H1-hESC	embryonic stem cell:	n/a	chr19:39574999-39575011 chr19:39575127-39575134 chr19:39575025-39575035 chr19:39575127-39575134 chr19:39575127-39575134 chr19:39575022-39575032 chr19:39575123-39575135
17	SIN3A	chr19:39574965-39575274	H1-hESC	embryonic stem cell:	n/a	n/a
18	JUND	chr19:39574995-39575213	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:39575027-39575077	GM12891	blood:	n/a
2	chr19:39575027-39575077	PFSK-1	brain:	n/a
3	chr19:39575027-39575077	K562	blood:	n/a
4	chr19:39575027-39575077	LNCaP	prostate:	n/a
5	chr19:39575027-39575077	GM19239	blood:	n/a
6	chr19:39575027-39575077	HUVEC	blood vessel:	n/a
7	chr19:39575027-39575077	Caco-2	colon:	n/a
8	chr19:39575027-39575077	SK-N-MC	brain:	n/a
9	chr19:39575027-39575077	MCF-7	breast:	n/a
10	chr19:39575027-39575077	ECC-1	luminal epithelium:	n/a
11	chr19:39575027-39575077	SKMC	muscle:	n/a
12	chr19:39575027-39575077	HMEC	breast:	n/a
13	chr19:39575027-39575077	PrEC	prostate:	n/a
14	chr19:39575027-39575077	HRE	kidney:	n/a
15	chr19:39575027-39575077	HepG2	liver:	n/a
16	chr19:39575027-39575077	NT2-D1	testis:	n/a
17	chr19:39575027-39575077	IMR90	lung:	fetal
18	chr19:39575027-39575077	HRCEpiC	kidney:	n/a
19	chr19:39575027-39575077	MCF10A-Er-Src	breast:	n/a
20	chr19:39575027-39575077	NH-A	brain:	n/a
21	chr19:39575027-39575077	U87	brain:	n/a
22	chr19:39575027-39575077	HEEpiC	esophagus:	n/a
23	chr19:39575027-39575077	NB4	blood:	n/a
24	chr19:39575027-39575077	HAEpiC	amniotic membrane:	n/a
25	chr19:39575027-39575077	HNPCEpiC	eye:	n/a
26	chr19:39575027-39575077	AG10803	skin:	n/a
27	chr19:39575027-39575077	AoSMC	blood vessel:	n/a
28	chr19:39575027-39575077	Hela-S3	cervix:	n/a
29	chr19:39575027-39575077	RPTEC	kidney:	n/a
30	chr19:39575027-39575077	HIPEpiC	eye:	n/a
31	chr19:39575027-39575077	HPAEpiC	pulmonary alveolar:	n/a
32	chr19:39575027-39575077	BE2_C	brain:	n/a
33	chr19:39575027-39575077	AG04449	skin:	fetal
34	chr19:39575027-39575077	AG04450	lung:	fetal
35	chr19:39575027-39575077	SK-N-SH	brain:	n/a
36	chr19:39575027-39575077	Hepatocyte	liver:	n/a
37	chr19:39575027-39575077	BJ	skin:	n/a
38	chr19:39575027-39575077	HCF	heart:	n/a
39	chr19:39575027-39575077	AG09309	skin:	n/a
40	chr19:39575027-39575077	PANC-1	pancreas:	n/a
41	chr19:39575027-39575077	Jurkat	blood:	n/a
42	chr19:39575027-39575077	NHBE	bronchial:	n/a
43	chr19:39575027-39575077	SK-N-SH_RA	brain:	n/a
44	chr19:39575027-39575077	ovcar-3	ovarian:	n/a
45	chr19:39575027-39575077	HRPEpiC	eye:	n/a
46	chr19:39575027-39575077	GM12892	blood:	n/a
47	chr19:39575027-39575077	NHDF-neo	bronchial:	n/a
48	chr19:39575027-39575077	H1-hESC	embryonic stem cell:	embryo
49	chr19:39575027-39575077	GM12878	blood:	n/a
50	chr19:39575027-39575077	AG09319	gingival:	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	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10408661	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12151180	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2569365	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34738600	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs377373	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs380679	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs384605	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs385681	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs392005	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs392135	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs393559	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs395387	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs396616	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs397189	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs400011	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs420682	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs426076	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs452666	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs453853	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802015	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4803196	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4803197	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs482679	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs487456	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs578940	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs597995	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs602744	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs609327	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs620642	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs621580	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs648192	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs648635	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs665998	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs690812	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs691059	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs691114	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]
rs691256	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs691266	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs691391	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]
rs691890	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs692294	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs692343	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs692347	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs774927	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs774928	0.96[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:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39573000-39575600	Flanking Active TSS	HMEC	breast
2	chr19:39573400-39575400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr19:39573400-39575400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr19:39573400-39575600	Active TSS	Brain Substantia Nigra	brain
5	chr19:39573600-39575200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr19:39573600-39575600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
7	chr19:39573800-39575200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
8	chr19:39573800-39575400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr19:39573800-39575400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr19:39574000-39575200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
11	chr19:39574000-39575400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
12	chr19:39574000-39575400	Flanking Active TSS	HUVEC	blood vessel
13	chr19:39574000-39575400	Active TSS	NHDF-Ad	bronchial
14	chr19:39574200-39575200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr19:39574200-39575200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:39574200-39575400	Active TSS	H9 Cell Line	embryonic stem cell
17	chr19:39574200-39575400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:39574200-39575600	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:39574200-39576400	Weak transcription	Right Atrium	heart
20	chr19:39574400-39575200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr19:39574400-39575200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
22	chr19:39574400-39575200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr19:39574400-39575200	Bivalent Enhancer	Fetal Muscle Leg	muscle
24	chr19:39574400-39575200	Enhancers	Pancreas	Pancrea
25	chr19:39574400-39575400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr19:39574400-39575400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr19:39574400-39575400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
28	chr19:39574400-39575400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
29	chr19:39574400-39575400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr19:39574400-39575400	Active TSS	Brain Anterior Caudate	brain
31	chr19:39574400-39575600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr19:39574400-39576000	Active TSS	Esophagus	oesophagus
33	chr19:39574600-39575200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr19:39574600-39575200	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:39574600-39575200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr19:39574600-39575200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
37	chr19:39574600-39575200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr19:39574600-39575200	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
39	chr19:39574600-39575200	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr19:39574600-39575200	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
41	chr19:39574600-39575200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
42	chr19:39574600-39575200	Bivalent/Poised TSS	HSMM	muscle
43	chr19:39574600-39575200	Active TSS	NHEK	skin
44	chr19:39574600-39575400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr19:39574600-39575400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr19:39574600-39575400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
47	chr19:39574600-39575400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr19:39574600-39575400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
49	chr19:39574600-39575400	Active TSS	Osteobl	bone
50	chr19:39574600-39575600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell

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