Variant report

Variant	rs4150589
Chromosome Location	chr11:18360251-18360252
allele	C/T
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	chr11:18357953-18360278	K562	blood:	n/a	n/a

Variant related genes	Relation type
GTF2H1	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10741740	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10741743	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10766467	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10766469	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10766471	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10832919	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10832920	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10832923	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024606	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11024613	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11024622	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12294486	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2037867	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2305564	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2403254	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3802967	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4150581	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4150606	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4150628	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4150644	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4150678	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4596	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60889939	0.88[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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv933836	chr11:18300254-18440933	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
4	nsv1047049	chr11:18359702-18520008	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv540955	chr11:18359702-18520008	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4150589	GTF2H1	cis	Nerve Tibial	GTEx
rs4150589	GTF2H1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18345000-18383200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:18345000-18405000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:18346800-18372000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:18346800-18382800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr11:18346800-18390400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr11:18347000-18372400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr11:18347000-18387400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr11:18347400-18366800	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr11:18347400-18371200	Strong transcription	Fetal Muscle Trunk	muscle
10	chr11:18347800-18368200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr11:18348000-18371200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr11:18348400-18365800	Strong transcription	Osteobl	bone
13	chr11:18350400-18371200	Strong transcription	Dnd41	blood
14	chr11:18350400-18372000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:18350400-18372000	Strong transcription	Liver	Liver
16	chr11:18350600-18371600	Strong transcription	Fetal Intestine Large	intestine
17	chr11:18350800-18361800	Strong transcription	Lung	lung
18	chr11:18350800-18371200	Strong transcription	Fetal Thymus	thymus
19	chr11:18350800-18371800	Strong transcription	Fetal Muscle Leg	muscle
20	chr11:18350800-18372200	Strong transcription	Placenta	Placenta
21	chr11:18351000-18368000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr11:18351200-18368200	Strong transcription	NH-A	brain
23	chr11:18351200-18373600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:18351200-18387000	Weak transcription	Stomach Mucosa	stomach
25	chr11:18351600-18362400	Weak transcription	Fetal Heart	heart
26	chr11:18351600-18368200	Strong transcription	NHEK	skin
27	chr11:18351600-18371200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr11:18351600-18371800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr11:18352000-18362000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr11:18352000-18366000	Strong transcription	Fetal Brain Female	brain
31	chr11:18352000-18368400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:18352200-18363200	Strong transcription	HepG2	liver
33	chr11:18352400-18371600	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr11:18352400-18389000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr11:18353200-18372200	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr11:18353400-18363400	Strong transcription	A549	lung
37	chr11:18353600-18361600	Strong transcription	NHDF-Ad	bronchial
38	chr11:18353800-18361000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr11:18353800-18366000	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr11:18353800-18368200	Strong transcription	Fetal Lung	lung
41	chr11:18353800-18368800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr11:18353800-18369600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr11:18353800-18372000	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr11:18354000-18363000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr11:18354000-18364000	Strong transcription	HUVEC	blood vessel
46	chr11:18354000-18370600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr11:18354000-18371800	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr11:18354000-18372200	Strong transcription	Adipose Nuclei	Adipose
49	chr11:18354200-18366800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr11:18354200-18368400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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