Variant report

Variant	rs11672724
Chromosome Location	chr19:38457488-38457489
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38396344..38398889-chr19:38454374..38457525,4	MCF-7	breast:
2	chr19:38457253..38459371-chr19:38481407..38483076,2	MCF-7	breast:
3	chr19:38455932..38458635-chr19:38458979..38461344,2	MCF-7	breast:
4	chr19:38395796..38398301-chr19:38456658..38458907,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171804	Chromatin interaction
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11083442	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11666497	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11667246	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668748	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11672257	0.86[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672673	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1807157	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2382624	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs241955	0.86[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs56672492	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59616348	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73029180	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73031215	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73034929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034946	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38453200-38457800	Genic enhancers	A549	lung
2	chr19:38454000-38458000	Weak transcription	Small Intestine	intestine
3	chr19:38454400-38460800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:38454400-38461200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr19:38454600-38460800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr19:38454600-38461000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr19:38454800-38459200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr19:38454800-38459200	Weak transcription	NHLF	lung
9	chr19:38455200-38459400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:38455200-38461400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr19:38456000-38461000	Weak transcription	Fetal Stomach	stomach
12	chr19:38456200-38459600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr19:38456400-38457600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr19:38456400-38457600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:38456400-38457800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr19:38456400-38457800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr19:38456400-38457800	Enhancers	Brain Substantia Nigra	brain
18	chr19:38456400-38457800	Enhancers	Duodenum Mucosa	Duodenum
19	chr19:38456400-38457800	Enhancers	Placenta	Placenta
20	chr19:38456400-38457800	Enhancers	NH-A	brain
21	chr19:38456400-38458000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:38456400-38458200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr19:38456400-38458400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:38456400-38459200	Genic enhancers	Fetal Intestine Small	intestine
25	chr19:38456600-38457600	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr19:38456600-38457600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:38456600-38457800	Strong transcription	Primary T cells from cord blood	blood
28	chr19:38456600-38457800	Enhancers	Brain Hippocampus Middle	brain
29	chr19:38456600-38458000	Genic enhancers	Primary B cells from peripheral blood	blood
30	chr19:38456600-38458000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr19:38456600-38458000	Enhancers	Fetal Intestine Large	intestine
32	chr19:38456600-38460800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr19:38456800-38457600	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr19:38456800-38457600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr19:38456800-38457600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr19:38456800-38457600	Flanking Active TSS	HMEC	breast
37	chr19:38456800-38457800	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr19:38456800-38457800	Enhancers	Colonic Mucosa	Colon
39	chr19:38456800-38457800	Enhancers	Gastric	stomach
40	chr19:38456800-38457800	Enhancers	Pancreas	Pancrea
41	chr19:38456800-38457800	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr19:38456800-38457800	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr19:38456800-38458200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr19:38456800-38458400	Enhancers	HepG2	liver
45	chr19:38457000-38457600	Enhancers	H1 Cell Line	embryonic stem cell
46	chr19:38457000-38457600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr19:38457000-38457600	Enhancers	NHDF-Ad	bronchial
48	chr19:38457000-38457800	Enhancers	Muscle Satellite Cultured Cells	--
49	chr19:38457000-38457800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr19:38457000-38457800	Enhancers	Stomach Mucosa	stomach

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