Variant report

Variant	rs3019233
Chromosome Location	chr11:77163500-77163501
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1225478	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1237490	0.85[EUR][1000 genomes]
rs2154754	0.87[EUR][1000 genomes]
rs2602476	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2602487	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3015982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3015983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3015985	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3015986	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3015988	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3015990	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3015992	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3019234	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3019235	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3019236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3019249	0.92[EUR][1000 genomes]
rs3019257	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34025917	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34880271	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs472691	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs476258	0.85[EUR][1000 genomes]
rs479104	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs493256	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs494289	0.87[EUR][1000 genomes]
rs503406	0.93[EUR][1000 genomes]
rs505841	0.84[EUR][1000 genomes]
rs508662	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs51500	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs520938	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs522015	0.93[EUR][1000 genomes]
rs523481	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs531638	0.89[EUR][1000 genomes]
rs535008	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs552323	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs557484	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs558470	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs560571	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs561386	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs562845	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs563731	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs572485	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs576220	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs580624	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs592602	0.87[EUR][1000 genomes]
rs595654	0.89[EUR][1000 genomes]
rs598801	0.91[EUR][1000 genomes]
rs644551	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs649040	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs653792	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs674259	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs683455	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs683762	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs684793	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs686068	0.91[EUR][1000 genomes]
rs689108	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7934230	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949721	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers 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	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS 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	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv3424135	chr11:76961603-77277087	Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1037724	chr11:77061945-77250391	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv541091	chr11:77061945-77250391	Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3437433	chr11:77101280-77291686	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77142200-77164800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:77149200-77165400	Weak transcription	Ovary	ovary
3	chr11:77152800-77166400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:77153600-77168600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr11:77155400-77181400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:77157000-77168400	Weak transcription	Small Intestine	intestine
7	chr11:77158200-77168600	Weak transcription	Stomach Mucosa	stomach
8	chr11:77158400-77169800	Weak transcription	Fetal Intestine Large	intestine
9	chr11:77158600-77164000	Weak transcription	Fetal Intestine Small	intestine
10	chr11:77159800-77168400	Weak transcription	Fetal Brain Female	brain
11	chr11:77160200-77169400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr11:77160600-77164800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr11:77160600-77165800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:77160600-77178000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr11:77160800-77167000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:77161000-77170200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr11:77161200-77167400	Weak transcription	Brain Hippocampus Middle	brain
18	chr11:77161200-77179200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr11:77162000-77163600	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr11:77162000-77165400	Weak transcription	Primary T cells from cord blood	blood
21	chr11:77162000-77165800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr11:77162200-77163800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr11:77162400-77164000	Enhancers	GM12878-XiMat	blood
24	chr11:77162400-77165000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr11:77162400-77166800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr11:77162400-77167000	Weak transcription	Primary B cells from cord blood	blood
27	chr11:77162400-77167200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr11:77162400-77167400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr11:77162400-77168000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr11:77162600-77165000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr11:77162600-77165600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr11:77162600-77165600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr11:77162600-77165800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr11:77162600-77166200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr11:77162600-77166400	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr11:77163000-77163600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr11:77163000-77164200	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr11:77163000-77173400	Weak transcription	Placenta	Placenta
39	chr11:77163200-77163600	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr11:77163200-77163800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
41	chr11:77163200-77163800	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr11:77163200-77164000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:77163400-77163600	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr11:77163400-77164000	Strong transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links