Variant report

Variant	rs17135547
Chromosome Location	chr11:77037399-77037400
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10082618	0.91[EUR][1000 genomes]
rs10501424	0.84[AFR][1000 genomes]
rs12294882	0.82[EUR][1000 genomes]
rs1453342	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs17135576	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs17135578	0.82[YRI][hapmap];0.94[AFR][1000 genomes]
rs17135582	1.00[AMR][1000 genomes]
rs17135589	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17135598	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1892788	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs2725829	0.83[TSI][hapmap]
rs7115397	1.00[TSI][hapmap];0.82[EUR][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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17135547	TPM2	trans	brain	seeQTL
rs17135547	TAGLN	trans	brain	seeQTL
rs17135547	S100A4	trans	brain	seeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77025400-77037600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:77027400-77043000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:77027600-77043000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr11:77028000-77068400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr11:77028200-77066000	Weak transcription	Fetal Kidney	kidney
6	chr11:77028400-77043000	Weak transcription	Fetal Lung	lung
7	chr11:77030400-77043000	Weak transcription	Colon Smooth Muscle	Colon
8	chr11:77030600-77086800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr11:77030800-77046800	Weak transcription	Small Intestine	intestine
10	chr11:77030800-77054200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr11:77031200-77043000	Weak transcription	Colonic Mucosa	Colon
12	chr11:77031400-77037600	Strong transcription	Primary T cells from cord blood	blood
13	chr11:77031600-77037800	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr11:77031600-77046600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr11:77031600-77066400	Weak transcription	Gastric	stomach
16	chr11:77031600-77073800	Weak transcription	Spleen	Spleen
17	chr11:77031800-77070400	Weak transcription	Fetal Brain Male	brain
18	chr11:77032000-77037600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:77032000-77037800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr11:77032000-77037800	Strong transcription	Duodenum Mucosa	Duodenum
21	chr11:77032000-77038000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:77032000-77038000	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr11:77032000-77038000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr11:77032200-77037800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr11:77032200-77066400	Weak transcription	Lung	lung
26	chr11:77032400-77037800	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr11:77032400-77043000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:77032600-77037600	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr11:77032600-77037800	Strong transcription	Placenta	Placenta
30	chr11:77032600-77043200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr11:77032600-77046200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr11:77032800-77037800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr11:77033000-77037800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr11:77033000-77038000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:77033200-77037800	Strong transcription	Fetal Stomach	stomach
36	chr11:77033200-77037800	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr11:77033400-77037600	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr11:77033400-77037600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr11:77033400-77067200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr11:77033400-77090400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr11:77033600-77046800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr11:77033800-77043000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr11:77033800-77043000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr11:77033800-77043000	Weak transcription	Esophagus	oesophagus
45	chr11:77033800-77043000	Weak transcription	NHEK	skin
46	chr11:77033800-77045200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr11:77033800-77059200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr11:77034000-77043000	Weak transcription	Brain Germinal Matrix	brain
49	chr11:77034000-77043000	Weak transcription	Fetal Muscle Trunk	muscle
50	chr11:77034400-77042600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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