Variant report

Variant	rs833917
Chromosome Location	chr19:38472344-38472345
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38420982..38422890-chr19:38471015..38472804,2	MCF-7	breast:
2	chr19:38421146..38425969-chr19:38469812..38473788,8	MCF-7	breast:
3	chr19:38471726..38473895-chr19:38475514..38478507,2	MCF-7	breast:
4	chr19:38470130..38474074-chr19:38479565..38484723,5	MCF-7	breast:
5	chr19:38417337..38419728-chr19:38472151..38473762,2	MCF-7	breast:
6	chr19:38429570..38433364-chr19:38470420..38473384,4	MCF-7	breast:
7	chr19:38464299..38466897-chr19:38471672..38473805,2	MCF-7	breast:
8	chr19:38469123..38470666-chr19:38472308..38474390,3	MCF-7	breast:
9	chr19:38394269..38398486-chr19:38470778..38473091,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000171804	Chromatin interaction
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1421676	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1421677	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2382623	0.86[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap]
rs4802150	0.81[EUR][1000 genomes]
rs6508753	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs697434	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs705496	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs705497	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7257190	0.80[EUR][1000 genomes]
rs7257688	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs8105305	0.80[EUR][1000 genomes]
rs8108245	0.83[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap]
rs941038	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38461600-38476600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:38461600-38493600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr19:38461600-38493600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr19:38461800-38476800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr19:38463600-38476000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:38463800-38476200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr19:38463800-38484800	Weak transcription	Fetal Stomach	stomach
8	chr19:38466000-38472400	Weak transcription	Primary T cells from cord blood	blood
9	chr19:38466000-38475800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr19:38468200-38473600	Enhancers	Lung	lung
11	chr19:38468200-38474200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr19:38468200-38474600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr19:38468200-38475600	Enhancers	HMEC	breast
14	chr19:38468200-38475800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:38468200-38483600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr19:38468400-38473000	Enhancers	NH-A	brain
17	chr19:38468400-38473200	Enhancers	HSMM	muscle
18	chr19:38468800-38474000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr19:38469000-38474200	Enhancers	Fetal Intestine Large	intestine
20	chr19:38469200-38474800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr19:38469200-38479600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr19:38469800-38475800	Genic enhancers	Fetal Intestine Small	intestine
23	chr19:38470000-38472800	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr19:38470200-38472600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:38470200-38473200	Enhancers	Fetal Lung	lung
26	chr19:38470200-38474200	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr19:38470200-38474200	Enhancers	Stomach Mucosa	stomach
28	chr19:38470200-38474400	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr19:38470400-38472400	Enhancers	Brain Angular Gyrus	brain
30	chr19:38470400-38472600	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr19:38470400-38473600	Enhancers	Pancreas	Pancrea
32	chr19:38470400-38474400	Enhancers	Esophagus	oesophagus
33	chr19:38470400-38474800	Enhancers	Gastric	stomach
34	chr19:38470600-38472600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr19:38470600-38473200	Enhancers	HSMMtube	muscle
36	chr19:38470600-38476000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr19:38470800-38472400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr19:38470800-38472400	Enhancers	A549	lung
39	chr19:38470800-38472600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr19:38470800-38473000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:38470800-38473600	Enhancers	Small Intestine	intestine
42	chr19:38470800-38474600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr19:38470800-38477200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr19:38470800-38494000	Weak transcription	Right Ventricle	heart
45	chr19:38471000-38472800	Enhancers	Fetal Kidney	kidney
46	chr19:38471000-38475400	Enhancers	NHEK	skin
47	chr19:38471000-38476800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr19:38471200-38472800	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr19:38471200-38474600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr19:38471200-38493800	Weak transcription	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links