Variant report

Variant	rs3804338
Chromosome Location	chr6:106772773-106772774
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	chr6:106751067..106754037-chr6:106772364..106773866,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252444	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10484576	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10485352	0.92[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11968933	1.00[ASW][hapmap]
rs12524358	0.91[ASN][1000 genomes]
rs12525660	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12526431	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[ASN][1000 genomes]
rs12526668	0.93[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12529488	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1415945	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17066826	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17066828	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17066837	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17066840	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17066847	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17066852	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17066855	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17587319	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17625939	0.94[ASN][1000 genomes]
rs2299860	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs28656919	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2883662	0.93[ASN][1000 genomes]
rs3761796	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3804332	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs3810872	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4028632	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4945745	0.91[ASN][1000 genomes]
rs4945746	0.91[ASN][1000 genomes]
rs4945748	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4946735	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4946736	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4946737	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4946738	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4946739	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4946741	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55682462	0.94[ASN][1000 genomes]
rs56204731	0.93[ASN][1000 genomes]
rs9373856	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1025900	chr6:106529777-106898421	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1018270	chr6:106531658-106908606	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv538399	chr6:106531658-106908606	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1035110	chr6:106557281-106802212	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv538400	chr6:106557281-106802212	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv1022855	chr6:106570926-106802072	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv538401	chr6:106570926-106802072	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	nsv1025963	chr6:106593639-106848778	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
11	nsv1020047	chr6:106597828-106912047	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
12	nsv970664	chr6:106635267-106887670	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	nsv1030367	chr6:106667748-106802072	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	nsv538403	chr6:106667748-106802072	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv870375	chr6:106696090-107047892	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3804338	PABPC3	trans	brain	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106735200-106773000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:106740000-106773000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:106771200-106774200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:106771400-106772800	Enhancers	Stomach Mucosa	stomach
5	chr6:106771400-106772800	Flanking Active TSS	Dnd41	blood
6	chr6:106771600-106772800	Enhancers	Brain Substantia Nigra	brain
7	chr6:106771600-106773200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:106771600-106773800	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr6:106771800-106772800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:106771800-106772800	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr6:106771800-106772800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr6:106771800-106772800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr6:106771800-106772800	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr6:106771800-106773000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr6:106772000-106772800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:106772000-106772800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr6:106772000-106772800	Enhancers	Fetal Brain Male	brain
18	chr6:106772000-106773000	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr6:106772000-106773000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr6:106772000-106773000	Flanking Active TSS	Liver	Liver
21	chr6:106772000-106773000	Weak transcription	Gastric	stomach
22	chr6:106772000-106773000	Weak transcription	Small Intestine	intestine
23	chr6:106772000-106773000	Weak transcription	Spleen	Spleen
24	chr6:106772000-106774000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:106772000-106774200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:106772000-106774200	Active TSS	K562	blood
27	chr6:106772200-106772800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:106772200-106772800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr6:106772200-106772800	Flanking Active TSS	HUVEC	blood vessel
30	chr6:106772200-106772800	Flanking Active TSS	NH-A	brain
31	chr6:106772200-106773000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr6:106772200-106773000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr6:106772200-106773000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr6:106772200-106773000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr6:106772200-106773000	Flanking Active TSS	Osteobl	bone
36	chr6:106772200-106773200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:106772200-106773200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:106772200-106773200	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr6:106772200-106773200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr6:106772200-106773400	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr6:106772200-106774000	Active TSS	H9 Cell Line	embryonic stem cell
42	chr6:106772200-106774200	Active TSS	Stomach Smooth Muscle	stomach
43	chr6:106772200-106774200	Active TSS	A549	lung
44	chr6:106772400-106772800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr6:106772400-106772800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr6:106772400-106772800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr6:106772400-106772800	Flanking Active TSS	Brain Cingulate Gyrus	brain
48	chr6:106772400-106772800	Flanking Active TSS	Fetal Lung	lung
49	chr6:106772400-106773000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr6:106772400-106773000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links