Variant report

Variant	rs56186790
Chromosome Location	chr19:52784806-52784807
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:52784799-52784849	HCM	heart:	n/a
2	chr19:52784799-52784849	MCF-7	breast:	n/a
3	chr19:52784799-52784849	RPTEC	kidney:	n/a
4	chr19:52784799-52784849	BE2_C	brain:	n/a
5	chr19:52784799-52784849	HepG2	liver:	n/a
6	chr19:52784799-52784849	PFSK-1	brain:	n/a
7	chr19:52784799-52784849	K562	blood:	n/a
8	chr19:52784799-52784849	ProgFib	skin:	n/a
9	chr19:52784799-52784849	PANC-1	pancreas:	n/a
10	chr19:52784799-52784849	Jurkat	blood:	n/a
11	chr19:52784799-52784849	NHBE	bronchial:	n/a
12	chr19:52784799-52784849	Caco-2	colon:	n/a
13	chr19:52784799-52784849	HCPEpiC	choroid plexus:	n/a
14	chr19:52784799-52784849	AG10803	skin:	n/a
15	chr19:52784799-52784849	NT2-D1	testis:	n/a
16	chr19:52784799-52784849	HCF	heart:	n/a
17	chr19:52784799-52784849	AG04449	skin:	fetal
18	chr19:52784799-52784849	HMEC	breast:	n/a
19	chr19:52784799-52784849	HCT-116	colon:	n/a
20	chr19:52784799-52784849	SKMC	muscle:	n/a
21	chr19:52784799-52784849	GM12891	blood:	n/a
22	chr19:52784799-52784849	PrEC	prostate:	n/a
23	chr19:52784799-52784849	GM12878	blood:	n/a
24	chr19:52784799-52784849	HIPEpiC	eye:	n/a
25	chr19:52784799-52784849	HEK293	kidney:	embryo
26	chr19:52784799-52784849	LNCaP	prostate:	n/a
27	chr19:52784799-52784849	BJ	skin:	n/a
28	chr19:52784799-52784849	HRPEpiC	eye:	n/a
29	chr19:52784799-52784849	HRE	kidney:	n/a
30	chr19:52784799-52784849	GM19239	blood:	n/a
31	chr19:52784799-52784849	AG04450	lung:	fetal
32	chr19:52784799-52784849	SK-N-SH_RA	brain:	n/a
33	chr19:52784799-52784849	AG09319	gingival:	n/a
34	chr19:52784799-52784849	AG09309	skin:	n/a
35	chr19:52784799-52784849	U87	brain:	n/a
36	chr19:52784799-52784849	T-47D	breast:	n/a
37	chr19:52784799-52784849	Hepatocyte	liver:	n/a
38	chr19:52784799-52784849	A549	lung:	n/a
39	chr19:52784799-52784849	SK-N-MC	brain:	n/a
40	chr19:52784799-52784849	AoSMC	blood vessel:	n/a
41	chr19:52784799-52784849	HRCEpiC	kidney:	n/a
42	chr19:52784799-52784849	CMK	blood:	n/a
43	chr19:52784799-52784849	NB4	blood:	n/a
44	chr19:52784799-52784849	H1-hESC	embryonic stem cell:	embryo
45	chr19:52784799-52784849	HPAEpiC	pulmonary alveolar:	n/a
46	chr19:52784799-52784849	HAEpiC	amniotic membrane:	n/a
47	chr19:52784799-52784849	HNPCEpiC	eye:	n/a
48	chr19:52784799-52784849	GM12892	blood:	n/a
49	chr19:52784799-52784849	SK-N-SH	brain:	n/a
50	chr19:52784799-52784849	HL-60	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52772026..52776261-chr19:52781637..52786393,5	K562	blood:

No data

Variant related genes	Relation type
MIR643	CpG island
ENSG00000196214	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1048399	1.00[ASN][1000 genomes]
rs55783720	1.00[ASN][1000 genomes]
rs62109258	1.00[ASN][1000 genomes]
rs62110401	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62110403	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62110407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110408	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62110409	1.00[ASN][1000 genomes]
rs62110410	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110415	1.00[ASN][1000 genomes]
rs62110447	1.00[ASN][1000 genomes]
rs749618	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv960862	chr19:52780307-52785546	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52774000-52786600	Weak transcription	Right Ventricle	heart
2	chr19:52774000-52787200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:52774200-52786600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr19:52774200-52797400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:52774200-52799600	Weak transcription	Hela-S3	cervix
6	chr19:52774400-52786600	Weak transcription	Osteobl	bone
7	chr19:52774400-52787000	Weak transcription	HUVEC	blood vessel
8	chr19:52774400-52787400	Weak transcription	NHDF-Ad	bronchial
9	chr19:52774600-52786400	Weak transcription	Brain Angular Gyrus	brain
10	chr19:52774600-52786600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr19:52774600-52795800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
12	chr19:52774800-52786400	Weak transcription	Brain Substantia Nigra	brain
13	chr19:52775000-52785400	Weak transcription	Gastric	stomach
14	chr19:52775000-52786400	Weak transcription	Brain Hippocampus Middle	brain
15	chr19:52775000-52786400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr19:52775000-52787400	Weak transcription	HepG2	liver
17	chr19:52775200-52786600	Weak transcription	Left Ventricle	heart
18	chr19:52777200-52787400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:52777200-52794000	Weak transcription	Psoas Muscle	Psoas
20	chr19:52777400-52786400	Weak transcription	Small Intestine	intestine
21	chr19:52777400-52787400	Weak transcription	Fetal Brain Male	brain
22	chr19:52777600-52785400	Weak transcription	Adipose Nuclei	Adipose
23	chr19:52777600-52786000	Weak transcription	NH-A	brain
24	chr19:52777600-52786800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:52777800-52785400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr19:52777800-52785600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr19:52777800-52785800	Weak transcription	K562	blood
28	chr19:52777800-52786000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr19:52777800-52786200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:52777800-52786400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr19:52777800-52786400	Weak transcription	Brain Anterior Caudate	brain
32	chr19:52777800-52786400	Weak transcription	HSMM	muscle
33	chr19:52777800-52786600	Weak transcription	Colon Smooth Muscle	Colon
34	chr19:52777800-52786600	Weak transcription	Pancreas	Pancrea
35	chr19:52777800-52786800	Weak transcription	HSMMtube	muscle
36	chr19:52777800-52787400	Weak transcription	Stomach Mucosa	stomach
37	chr19:52777800-52787800	Weak transcription	HMEC	breast
38	chr19:52778000-52785800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr19:52778000-52786800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr19:52778400-52786000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr19:52778400-52786400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr19:52780000-52785000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr19:52780000-52786200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr19:52780000-52786600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr19:52780200-52785400	Weak transcription	Aorta	Aorta
46	chr19:52780200-52786600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr19:52780400-52785800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr19:52780400-52786400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr19:52780400-52786600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr19:52780400-52786600	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links