Variant report

Variant	rs4803708
Chromosome Location	chr19:38553206-38553207
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	chr19:38543891..38548790-chr19:38549215..38554298,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221258	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1630393	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654346	0.88[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1654351	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654353	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725471	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1725476	0.86[AFR][1000 genomes]
rs7249265	0.82[CHB][hapmap]
rs855635	0.95[AMR][1000 genomes];0.89[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	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1062518	chr19:38540454-38564913	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38522000-38553600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr19:38528200-38573200	Weak transcription	Left Ventricle	heart
3	chr19:38539000-38572000	Weak transcription	Right Ventricle	heart
4	chr19:38539200-38591200	Weak transcription	Small Intestine	intestine
5	chr19:38543400-38553600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:38543800-38563200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr19:38545800-38553600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr19:38546400-38553600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr19:38546600-38553600	Weak transcription	Brain Substantia Nigra	brain
10	chr19:38546600-38554000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr19:38546600-38572200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr19:38547000-38553400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr19:38547000-38553600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:38547000-38554800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr19:38547000-38563600	Weak transcription	Fetal Lung	lung
16	chr19:38547200-38561400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr19:38548600-38554400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr19:38548600-38555000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr19:38549000-38553600	Weak transcription	Brain Hippocampus Middle	brain
20	chr19:38549200-38553400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr19:38549200-38564800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr19:38549200-38572000	Weak transcription	Liver	Liver
23	chr19:38549400-38553600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr19:38549400-38560000	Weak transcription	Psoas Muscle	Psoas
25	chr19:38549600-38553600	Weak transcription	Esophagus	oesophagus
26	chr19:38549600-38572600	Weak transcription	Thymus	Thymus
27	chr19:38550000-38561000	Weak transcription	Hela-S3	cervix
28	chr19:38550000-38570400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr19:38550800-38563400	Weak transcription	Spleen	Spleen
30	chr19:38550800-38565200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr19:38550800-38570000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr19:38550800-38572200	Weak transcription	Colonic Mucosa	Colon
33	chr19:38550800-38590000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr19:38551000-38556000	Genic enhancers	Primary B cells from peripheral blood	blood
35	chr19:38551000-38572000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr19:38551200-38553600	Weak transcription	Fetal Kidney	kidney
37	chr19:38551200-38555600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr19:38551200-38562200	Weak transcription	Primary T cells from cord blood	blood
39	chr19:38551200-38562600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr19:38551200-38563600	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr19:38551200-38567000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr19:38551200-38613800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr19:38551400-38562400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr19:38551400-38567000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr19:38551600-38553800	Enhancers	NH-A	brain
46	chr19:38551600-38554800	Enhancers	HSMM	muscle
47	chr19:38551800-38554600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:38551800-38555000	Enhancers	Fetal Muscle Leg	muscle
49	chr19:38552200-38554200	Enhancers	Pancreas	Pancrea
50	chr19:38552200-38555000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links