Variant report

Variant	rs2560904
Chromosome Location	chr19:52785945-52785946
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52785054..52786730-chr19:52799548..52801904,2	K562	blood:
2	chr19:52772026..52776261-chr19:52781637..52786393,5	K562	blood:

Variant related genes	Relation type
ENSG00000269102	Chromatin interaction
ENSG00000196214	Chromatin interaction
ENSG00000198464	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10426950	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2560875	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2560905	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2657927	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2657928	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41497444	0.80[ASN][1000 genomes]
rs62110405	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:125 , 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	chr19:52775000-52786400	Weak transcription	Brain Hippocampus Middle	brain
14	chr19:52775000-52786400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr19:52775000-52787400	Weak transcription	HepG2	liver
16	chr19:52775200-52786600	Weak transcription	Left Ventricle	heart
17	chr19:52777200-52787400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:52777200-52794000	Weak transcription	Psoas Muscle	Psoas
19	chr19:52777400-52786400	Weak transcription	Small Intestine	intestine
20	chr19:52777400-52787400	Weak transcription	Fetal Brain Male	brain
21	chr19:52777600-52786000	Weak transcription	NH-A	brain
22	chr19:52777600-52786800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr19:52777800-52786000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr19:52777800-52786200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr19:52777800-52786400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:52777800-52786400	Weak transcription	Brain Anterior Caudate	brain
27	chr19:52777800-52786400	Weak transcription	HSMM	muscle
28	chr19:52777800-52786600	Weak transcription	Colon Smooth Muscle	Colon
29	chr19:52777800-52786600	Weak transcription	Pancreas	Pancrea
30	chr19:52777800-52786800	Weak transcription	HSMMtube	muscle
31	chr19:52777800-52787400	Weak transcription	Stomach Mucosa	stomach
32	chr19:52777800-52787800	Weak transcription	HMEC	breast
33	chr19:52778000-52786800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr19:52778400-52786000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr19:52778400-52786400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr19:52780000-52786200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr19:52780000-52786600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr19:52780200-52786600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr19:52780400-52786400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr19:52780400-52786600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr19:52780400-52786600	Weak transcription	Ovary	ovary
42	chr19:52780400-52786600	Weak transcription	NHLF	lung
43	chr19:52780400-52800000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr19:52780600-52787000	Weak transcription	NHEK	skin
45	chr19:52781000-52787400	Weak transcription	Colonic Mucosa	Colon
46	chr19:52781200-52786400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr19:52781400-52786400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr19:52781400-52786400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr19:52781600-52793600	Weak transcription	Fetal Heart	heart
50	chr19:52781800-52787200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links