Variant report

Variant	rs647235
Chromosome Location	chr11:77566849-77566850
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs108843	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10899396	0.85[ASN][1000 genomes]
rs10899397	0.85[ASN][1000 genomes]
rs10899401	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10899414	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11237264	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11237279	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12294668	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12418931	0.85[ASN][1000 genomes]
rs1783547	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2508184	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35711367	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs570786	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs581807	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs582866	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs584732	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585172	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585721	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs591283	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598933	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs600968	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs601551	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs603462	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608389	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs608539	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609151	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs611671	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs611906	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs636041	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs649671	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs658398	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs667213	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675925	0.86[AFR][1000 genomes]
rs679155	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs679526	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs685474	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs694893	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7925289	0.85[ASN][1000 genomes]
rs7929313	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7936105	0.93[ASN][1000 genomes]
rs9667706	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050891	chr11:77416645-77788002	Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1037292	chr11:77431583-77745934	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription 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 miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv541092	chr11:77431583-77745934	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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 target site	26 gene(s)	inside rSNPs	diseases
4	nsv949316	chr11:77454076-77769885	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv520740	chr11:77553638-77997936	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs647235	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77548800-77582800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr11:77560800-77568400	Strong transcription	Skeletal Muscle Female	skeletal muscle
3	chr11:77562600-77568000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
4	chr11:77563000-77567600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr11:77563000-77569000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
6	chr11:77563400-77568400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:77563400-77568400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr11:77563600-77568400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
9	chr11:77564000-77568400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
10	chr11:77564200-77567200	ZNF genes & repeats	Fetal Intestine Small	intestine
11	chr11:77564200-77567400	ZNF genes & repeats	Fetal Intestine Large	intestine
12	chr11:77564400-77567400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:77564400-77567800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:77564400-77568000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
15	chr11:77564400-77568400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr11:77564400-77568400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr11:77564600-77567600	ZNF genes & repeats	Brain Germinal Matrix	brain
18	chr11:77565200-77567600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
19	chr11:77565200-77568400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
20	chr11:77565400-77567000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
21	chr11:77565400-77567000	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
22	chr11:77565400-77567000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr11:77565400-77567000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
24	chr11:77565400-77567200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
25	chr11:77565400-77567200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr11:77565400-77567200	ZNF genes & repeats	Fetal Thymus	thymus
27	chr11:77565400-77567400	ZNF genes & repeats	Placenta	Placenta
28	chr11:77565400-77567400	Strong transcription	Stomach Smooth Muscle	stomach
29	chr11:77565400-77567600	ZNF genes & repeats	Primary T cells from cord blood	blood
30	chr11:77565400-77567600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
31	chr11:77565400-77567600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr11:77565400-77567800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
33	chr11:77565400-77567800	ZNF genes & repeats	Fetal Brain Female	brain
34	chr11:77565400-77568000	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr11:77565400-77568200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:77565400-77568200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
37	chr11:77565400-77568200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr11:77565400-77568600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr11:77565400-77569200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr11:77565600-77567000	ZNF genes & repeats	Fetal Stomach	stomach
41	chr11:77565600-77567000	ZNF genes & repeats	HUVEC	blood vessel
42	chr11:77565600-77567800	ZNF genes & repeats	Primary B cells from cord blood	blood
43	chr11:77565600-77568400	Strong transcription	Placenta Amnion	Placenta Amnion
44	chr11:77565800-77567000	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr11:77566000-77567000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr11:77566000-77568400	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr11:77566000-77592600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr11:77566200-77567000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr11:77566200-77567000	Weak transcription	Fetal Kidney	kidney
50	chr11:77566200-77567000	Weak transcription	Gastric	stomach

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