Variant report

Variant	rs3790078
Chromosome Location	chr16:69906182-69906183
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:69906020..69907607-chr16:69913429..69915841,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10852461	0.84[EUR][1000 genomes]
rs11075744	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12446168	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12446197	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12598642	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12919094	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12921407	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12926791	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12927052	0.83[AMR][1000 genomes]
rs12927431	0.83[AMR][1000 genomes]
rs1500337	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1566453	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1566454	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1566455	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2102067	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2291959	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2362641	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2362642	0.84[EUR][1000 genomes]
rs2937121	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3790075	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3790076	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3790080	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4146819	0.84[EUR][1000 genomes]
rs4296254	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4985448	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4985449	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6499263	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6499268	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6499269	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6499270	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7190013	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7192213	0.81[EUR][1000 genomes]
rs7193038	0.84[EUR][1000 genomes]
rs7196842	0.82[EUR][1000 genomes]
rs8044876	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8047682	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8048550	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8049373	0.83[EUR][1000 genomes]
rs8050414	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8051168	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8052225	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8060478	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9940315	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1062171	chr16:69854267-70188585	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv542941	chr16:69854267-70188585	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv1059249	chr16:69854467-70188446	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	nsv542942	chr16:69854467-70188446	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2758428	chr16:69855122-70313222	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2758652	chr16:69855122-70313222	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv960355	chr16:69901844-69907446	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3790078	LOC440348	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69834000-69910600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr16:69890400-69923400	Weak transcription	HUVEC	blood vessel
3	chr16:69893000-69906800	Weak transcription	GM12878-XiMat	blood
4	chr16:69893000-69907000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr16:69893000-69934800	Weak transcription	Hela-S3	cervix
6	chr16:69893200-69906400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr16:69893200-69923000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr16:69893400-69906400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr16:69893600-69910600	Weak transcription	A549	lung
10	chr16:69895600-69906200	Weak transcription	Fetal Brain Female	brain
11	chr16:69895800-69907000	Weak transcription	Small Intestine	intestine
12	chr16:69896000-69906200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr16:69896000-69906400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr16:69896000-69906400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr16:69896000-69909400	Weak transcription	Fetal Kidney	kidney
16	chr16:69896400-69906600	Weak transcription	Stomach Mucosa	stomach
17	chr16:69896400-69910000	Weak transcription	Fetal Lung	lung
18	chr16:69896600-69906600	Weak transcription	Colon Smooth Muscle	Colon
19	chr16:69896600-69909200	Strong transcription	Fetal Intestine Small	intestine
20	chr16:69896600-69910200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr16:69896800-69907200	Weak transcription	Right Atrium	heart
22	chr16:69897000-69906400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr16:69900000-69906400	Weak transcription	NHDF-Ad	bronchial
24	chr16:69900000-69914600	Weak transcription	NHLF	lung
25	chr16:69900200-69910000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr16:69900200-69914600	Weak transcription	NH-A	brain
27	chr16:69900800-69915600	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr16:69900800-69933400	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr16:69901000-69910000	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr16:69901000-69910600	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr16:69901000-69910600	Strong transcription	Duodenum Mucosa	Duodenum
32	chr16:69901000-69912600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr16:69901000-69915200	Strong transcription	Primary B cells from peripheral blood	blood
34	chr16:69901000-69915200	Strong transcription	Primary T cells from cord blood	blood
35	chr16:69901000-69918800	Strong transcription	Fetal Intestine Large	intestine
36	chr16:69901200-69909600	Strong transcription	Primary B cells from cord blood	blood
37	chr16:69901200-69910200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr16:69901800-69907400	Weak transcription	K562	blood
39	chr16:69901800-69922000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr16:69901800-69924600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr16:69902000-69906400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr16:69902000-69910800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr16:69902000-69912400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr16:69902200-69906600	Weak transcription	Osteobl	bone
45	chr16:69902400-69906400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr16:69902600-69914400	Weak transcription	HSMM	muscle
47	chr16:69902600-69924800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr16:69902800-69906400	Weak transcription	Fetal Muscle Leg	muscle
49	chr16:69902800-69906600	Weak transcription	HSMMtube	muscle
50	chr16:69902800-69910800	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links