Variant report

Variant	rs11128928
Chromosome Location	chr3:19990813-19990814
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:19986589-19991063	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr3:19986265-20000717	K562	blood:	n/a	n/a
3	POLR2A	chr3:19990602-19991443	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr3:19990061-19991082	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:19987841-19990881	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:19986921..19992254-chr3:20078952..20084327,16	K562	blood:
2	chr3:19987383..19992426-chr3:20011245..20019650,13	MCF-7	breast:
3	chr3:19987439..19992261-chr3:20226257..20229350,4	K562	blood:
4	chr3:19986985..19992254-chr3:20079680..20083856,14	K562	blood:

Variant related genes	Relation type
EFHB	TF binding region
RAB5A	TF binding region
ENSG00000114166	Chromatin interaction
ENSG00000129810	Chromatin interaction
ENSG00000144566	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11128927	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11128929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11128930	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11128931	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1143451	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12629485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12631435	0.82[EUR][1000 genomes]
rs13065319	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13068289	0.81[EUR][1000 genomes]
rs13070718	0.83[EUR][1000 genomes]
rs13072891	0.90[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs13076973	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13077307	0.87[ASN][1000 genomes]
rs13078505	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13082980	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13086159	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13089853	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13093485	0.81[EUR][1000 genomes]
rs13097697	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13098388	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17181400	0.94[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17181862	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17796115	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34305656	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34343204	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34417128	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34705953	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34872212	0.81[EUR][1000 genomes]
rs35175665	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35482904	0.81[ASN][1000 genomes]
rs35684714	0.81[EUR][1000 genomes]
rs35713165	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4610240	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58859849	0.84[ASN][1000 genomes]
rs59086970	0.89[ASN][1000 genomes]
rs59608170	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60255931	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6796425	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71316239	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7434271	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7614695	0.84[ASN][1000 genomes]
rs7615145	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7618928	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7633940	0.84[ASN][1000 genomes]
rs7634934	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7646128	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9877801	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9878879	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats 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	17 gene(s)	inside rSNPs	diseases
6	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers 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 miRNA target site	17 gene(s)	inside rSNPs	diseases
7	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11128928	EFHB	cis	Skin Sun Exposed Lower leg	GTEx
rs11128928	EFHB	cis	Artery Tibial	GTEx
rs11128928	EFHB	cis	cerebellum	SCAN
rs11128928	EFHB	cis	parietal	SCAN
rs11128928	EFHB	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19987200-19991800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:19987400-19991400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:19987600-19991000	Active TSS	NHLF	lung
4	chr3:19987600-19991600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:19987800-19991400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr3:19987800-19991400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:19988000-19991200	Active TSS	H1 Cell Line	embryonic stem cell
8	chr3:19988000-19991400	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr3:19988200-19991600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:19988200-19991600	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr3:19989400-19991000	Flanking Active TSS	Fetal Brain Female	brain
12	chr3:19989400-19991400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:19989600-19991000	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr3:19989600-19991000	Flanking Active TSS	Dnd41	blood
15	chr3:19989600-19991200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:19989600-19991400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:19989800-19991200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr3:19989800-19991200	Weak transcription	Lung	lung
19	chr3:19989800-19991800	Weak transcription	Small Intestine	intestine
20	chr3:19989800-19993000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:19989800-19993000	Weak transcription	Esophagus	oesophagus
22	chr3:19989800-19993000	Weak transcription	Spleen	Spleen
23	chr3:19989800-19995000	Weak transcription	Gastric	stomach
24	chr3:19989800-20018800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:19990000-19991000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:19990000-19991000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:19990000-19991000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr3:19990000-19991000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr3:19990000-19991000	Flanking Active TSS	Fetal Lung	lung
30	chr3:19990000-19991200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr3:19990000-19991200	Enhancers	Fetal Heart	heart
32	chr3:19990000-19991400	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr3:19990000-19991400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:19990000-19991400	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr3:19990000-19991400	Flanking Active TSS	HUVEC	blood vessel
36	chr3:19990000-19991800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr3:19990000-19991800	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr3:19990000-19991800	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr3:19990000-19991800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr3:19990000-19992600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:19990000-19993400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr3:19990000-20008600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:19990000-20016200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr3:19990200-19991000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr3:19990200-19991000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:19990200-19991000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:19990200-19991000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:19990200-19991000	Enhancers	Brain Substantia Nigra	brain
49	chr3:19990200-19991000	Enhancers	Colon Smooth Muscle	Colon
50	chr3:19990200-19991000	Flanking Active TSS	Duodenum Mucosa	Duodenum

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