Variant report

Variant	rs2140551
Chromosome Location	chr2:48822381-48822382
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48822120..48826399-chr2:48830586..48834373,3	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 30 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10865231	1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs13007591	0.80[GIH][hapmap]
rs2293276	0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2882085	0.90[JPT][hapmap]
rs7574549	0.95[CHB][hapmap]

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	nsv1005954	chr2:48692696-48905723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535682	chr2:48692696-48905723	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv833981	chr2:48705444-48878179	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv581776	chr2:48763382-48913019	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1010494	chr2:48767055-49027310	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv1004965	chr2:48796170-49443587	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv535684	chr2:48796170-49443587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv498119	chr2:48808834-49422647	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv829197	chr2:48812496-48824109	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv833992	chr2:48814223-48998037	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:30)

SNP	Gene	Cis/trans	Tissue	Source
rs2140551	GTF2A1L	cis	Adipose Subcutaneous	GTEx
rs2140551	STON1-GTF2A1L	cis	Esophagus Mucosa	GTEx
rs2140551	STON1-GTF2A1L	cis	lung	GTEx
rs2140551	STON1	cis	Esophagus Muscularis	GTEx
rs2140551	STON1,GTF2A1L,FLJ46838,STON1-GTF2A1L	cis	substantia nigra	BrainEAC
rs2140551	STON1,GTF2A1L,FLJ46838,STON1-GTF2A1L	cis	intralobular white matter	BrainEAC
rs2140551	STON1-GTF2A1L	cis	Adipose Subcutaneous	GTEx
rs2140551	Contig42306_RC	trans	multi-tissue	Pritchard
rs2140551	STON1-GTF2A1L	cis	Liver	GTEx
rs2140551	STON1,GTF2A1L,FLJ46838,STON1-GTF2A1L	cis	occipital cortex	BrainEAC
rs2140551	STON1-GTF2A1L	cis	Artery Aorta	GTEx
rs2140551	GTF2A1L	cis	Esophagus Muscularis	GTEx
rs2140551	STON1,GTF2A1L,FLJ46838,STON1-GTF2A1L	cis	putamen	BrainEAC
rs2140551	GTF2A1L	cis	lung	GTEx
rs2140551	STON1-GTF2A1L	cis	Esophagus Muscularis	GTEx
rs2140551	STON1-GTF2A1L	cis	Nerve Tibial	GTEx
rs2140551	GTF2A1L	cis	Liver	GTEx
rs2140551	STON1,GTF2A1L,FLJ46838,STON1-GTF2A1L	cis	brain	BrainEAC
rs2140551	STON1-GTF2A1L	cis	cerebellum	SCAN
rs2140551	FSHR	cis	Esophagus Muscularis	GTEx
rs2140551	STON1,GTF2A1L,FLJ46838,STON1-GTF2A1L	cis	thalamus	BrainEAC
rs2140551	GTF2A1L	cis	Artery Tibial	GTEx
rs2140551	STON1,GTF2A1L,FLJ46838,STON1-GTF2A1L	cis	inferior olivary nucleus	BrainEAC
rs2140551	STON1,GTF2A1L,FLJ46838,STON1-GTF2A1L	cis	hippocampus	BrainEAC
rs2140551	STON1-GTF2A1L	cis	Stomach	GTEx
rs2140551	STON1-GTF2A1L	cis	Artery Tibial	GTEx
rs2140551	STON1-GTF2A1L	cis	parietal	SCAN
rs2140551	STON1,GTF2A1L,FLJ46838,STON1-GTF2A1L	cis	cerebellar cortex	BrainEAC
rs2140551	KLRAQ1	cis	parietal	SCAN
rs2140551	GTF2A1L	cis	Esophagus Mucosa	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48759000-48827600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr2:48794400-48827200	Weak transcription	NHDF-Ad	bronchial
3	chr2:48795600-48826000	Weak transcription	Fetal Intestine Small	intestine
4	chr2:48799000-48825800	Weak transcription	HSMMtube	muscle
5	chr2:48804600-48824600	Weak transcription	Fetal Intestine Large	intestine
6	chr2:48808400-48827600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:48808600-48834800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:48809000-48824400	Weak transcription	Left Ventricle	heart
9	chr2:48809600-48827200	Weak transcription	Right Ventricle	heart
10	chr2:48809800-48828600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:48812200-48828000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:48812400-48822800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:48812400-48824000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:48812400-48824200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:48813600-48828200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:48814000-48835600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:48814200-48834800	Weak transcription	Lung	lung
18	chr2:48815000-48826400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:48815200-48824000	Weak transcription	Fetal Stomach	stomach
20	chr2:48815800-48824400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:48815800-48840200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:48816200-48822600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:48816200-48834800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:48816400-48824200	Weak transcription	Placenta	Placenta
25	chr2:48816400-48824400	Weak transcription	Fetal Muscle Leg	muscle
26	chr2:48816400-48827200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr2:48816400-48833800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr2:48816400-48836200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:48816800-48824200	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:48817200-48824800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:48817400-48822800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr2:48818200-48825200	Weak transcription	Gastric	stomach
33	chr2:48818600-48822800	Strong transcription	Stomach Smooth Muscle	stomach
34	chr2:48818800-48823200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:48818800-48825800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:48819400-48824400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:48821000-48822800	Strong transcription	Ovary	ovary
38	chr2:48821000-48823200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:48821000-48823400	Strong transcription	Adipose Nuclei	Adipose
40	chr2:48821000-48825200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:48821400-48827200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:48821400-48830600	Weak transcription	Aorta	Aorta
43	chr2:48821600-48832400	Weak transcription	Fetal Kidney	kidney
44	chr2:48821800-48824200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:48821800-48824400	Weak transcription	Fetal Brain Male	brain
46	chr2:48822200-48822800	Enhancers	K562	blood
47	chr2:48822200-48823000	Strong transcription	Fetal Lung	lung

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