Variant report

Variant	rs4801955
Chromosome Location	chr19:39418485-39418486
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39414900..39416436-chr19:39417401..39420305,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11670675	0.82[EUR][1000 genomes]
rs12971945	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12972128	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12972744	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12975517	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12977011	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12978262	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12985277	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12985768	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2278413	0.84[EUR][1000 genomes]
rs35444792	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4801967	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803046	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6508829	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4801955	CTC-360G5.9	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39391200-39420800	Weak transcription	Small Intestine	intestine
2	chr19:39391600-39420600	Weak transcription	Right Atrium	heart
3	chr19:39392600-39418800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:39398000-39420600	Weak transcription	Psoas Muscle	Psoas
5	chr19:39402800-39420200	Weak transcription	Colon Smooth Muscle	Colon
6	chr19:39403600-39420400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr19:39403800-39420200	Weak transcription	Fetal Brain Male	brain
8	chr19:39406400-39420000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr19:39406800-39420200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr19:39409200-39419000	Strong transcription	Fetal Intestine Small	intestine
11	chr19:39409200-39420400	Weak transcription	Stomach Mucosa	stomach
12	chr19:39411400-39419000	Strong transcription	Fetal Stomach	stomach
13	chr19:39411600-39420400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:39411600-39420400	Weak transcription	Fetal Heart	heart
15	chr19:39412000-39419000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr19:39412000-39419600	Strong transcription	Fetal Muscle Leg	muscle
17	chr19:39412200-39419200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:39412800-39420600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr19:39413200-39418800	Weak transcription	GM12878-XiMat	blood
20	chr19:39413200-39420200	Weak transcription	Primary B cells from cord blood	blood
21	chr19:39413200-39420200	Weak transcription	NH-A	brain
22	chr19:39413200-39420200	Weak transcription	NHLF	lung
23	chr19:39413200-39420400	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr19:39413200-39420400	Weak transcription	Fetal Kidney	kidney
25	chr19:39413200-39420800	Weak transcription	Aorta	Aorta
26	chr19:39414400-39418600	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr19:39414400-39419400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr19:39414800-39419200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:39415200-39418600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr19:39415400-39420000	Weak transcription	NHEK	skin
31	chr19:39415400-39420200	Weak transcription	NHDF-Ad	bronchial
32	chr19:39415600-39420200	Weak transcription	Brain Angular Gyrus	brain
33	chr19:39415600-39420400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr19:39415600-39420400	Weak transcription	Colonic Mucosa	Colon
35	chr19:39415600-39420600	Weak transcription	Pancreas	Pancrea
36	chr19:39415800-39419600	Weak transcription	K562	blood
37	chr19:39415800-39420200	Weak transcription	Primary T cells from cord blood	blood
38	chr19:39415800-39420200	Weak transcription	HUVEC	blood vessel
39	chr19:39415800-39420400	Weak transcription	HSMM	muscle
40	chr19:39416200-39420200	Weak transcription	Brain Substantia Nigra	brain
41	chr19:39416200-39420200	Weak transcription	Osteobl	bone
42	chr19:39416400-39419800	Weak transcription	Left Ventricle	heart
43	chr19:39416400-39420000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr19:39416400-39420000	Weak transcription	Adipose Nuclei	Adipose
45	chr19:39416400-39420200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr19:39416400-39420200	Weak transcription	Brain Hippocampus Middle	brain
47	chr19:39416400-39420200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr19:39416400-39420200	Weak transcription	HMEC	breast
49	chr19:39416400-39420400	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr19:39416400-39420400	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links