Variant report

Variant	rs3784099
Chromosome Location	chr14:68749927-68749928
allele	A/G
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:68408216..68412729-chr14:68747829..68750873,4	MCF-7	breast:
2	chr14:68748043..68750359-chr14:69093901..69097127,3	MCF-7	breast:
3	chr14:68748170..68751386-chr14:68933626..68937180,4	MCF-7	breast:
4	chr14:68748548..68751029-chr14:68932619..68934768,2	MCF-7	breast:
5	chr14:68748777..68751807-chr14:69257794..69259818,3	MCF-7	breast:
6	chr14:68749573..68752589-chr14:68864032..68866537,3	MCF-7	breast:
7	chr14:68612521..68615403-chr14:68749154..68751195,2	MCF-7	breast:
8	chr14:68744987..68750260-chr14:69250111..69256950,7	MCF-7	breast:
9	chr14:68739540..68742303-chr14:68747560..68750666,4	MCF-7	breast:
10	chr14:68727081..68730048-chr14:68748759..68751215,2	MCF-7	breast:
11	chr14:68745338..68754336-chr14:69258355..69264353,12	MCF-7	breast:
12	chr14:68749358..68751013-chr14:68751341..68753019,2	MCF-7	breast:
13	chr14:68742486..68746272-chr14:68747119..68750722,4	MCF-7	breast:
14	chr14:68749379..68750879-chr14:68753293..68755908,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000185650	Chromatin interaction
ENSG00000259038	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10129646	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10131490	0.92[EUR][1000 genomes]
rs10483807	0.85[LWK][hapmap]
rs11158730	0.85[LWK][hapmap]
rs12880109	0.85[LWK][hapmap]
rs17105278	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs1885013	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1950897	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1956532	0.86[LWK][hapmap]
rs1957569	0.83[AMR][1000 genomes]
rs1957570	0.91[CEU][hapmap];0.91[GIH][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2013413	0.85[LWK][hapmap]
rs2104047	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2208397	0.95[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs28498223	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7148416	0.93[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7148882	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8008961	0.95[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs8015139	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs911254	0.85[LWK][hapmap]
rs911263	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv869154	chr14:68366754-69041768	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv428628	chr14:68674504-68835127	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Breast cancer (survival)	22232737	GWAS catalog

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68739000-68750000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr14:68740000-68750200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr14:68740000-68751600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr14:68742600-68751800	Weak transcription	Stomach Mucosa	stomach
5	chr14:68744800-68751400	Enhancers	HepG2	liver
6	chr14:68745600-68753400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr14:68746000-68750000	Weak transcription	Pancreas	Pancrea
8	chr14:68746000-68751600	Weak transcription	HSMMtube	muscle
9	chr14:68746000-68752800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr14:68746000-68758600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr14:68746200-68750000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr14:68746200-68750000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr14:68746200-68750000	Weak transcription	Brain Anterior Caudate	brain
14	chr14:68746200-68750000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr14:68746200-68750000	Weak transcription	Brain Substantia Nigra	brain
16	chr14:68746200-68750000	Weak transcription	Fetal Kidney	kidney
17	chr14:68746200-68751000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr14:68746200-68751400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr14:68746200-68751800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr14:68746200-68752000	Weak transcription	K562	blood
21	chr14:68746600-68764600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr14:68746800-68750000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr14:68746800-68750000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr14:68746800-68751600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr14:68747000-68754000	Enhancers	Primary T cells fromperipheralblood	blood
26	chr14:68747000-68755200	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr14:68747200-68755200	Enhancers	Primary B cells from peripheral blood	blood
28	chr14:68747400-68750000	Enhancers	Primary B cells from cord blood	blood
29	chr14:68747400-68750000	Weak transcription	Psoas Muscle	Psoas
30	chr14:68747400-68754000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr14:68747600-68750200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr14:68748200-68750000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr14:68748200-68753600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr14:68748400-68750000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr14:68748400-68755400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr14:68749000-68750600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr14:68749000-68750600	Enhancers	Brain Hippocampus Middle	brain
38	chr14:68749000-68750600	Enhancers	Small Intestine	intestine
39	chr14:68749000-68751000	Enhancers	Fetal Intestine Large	intestine
40	chr14:68749000-68751600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr14:68749000-68753400	Enhancers	Primary hematopoietic stem cells	blood
42	chr14:68749000-68753400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr14:68749000-68754000	Enhancers	Fetal Thymus	thymus
44	chr14:68749200-68750000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr14:68749200-68750200	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr14:68749200-68750600	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr14:68749200-68750800	Enhancers	Fetal Intestine Small	intestine
48	chr14:68749200-68751000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr14:68749200-68751000	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr14:68749200-68752200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links