Variant report

Variant	rs993867
Chromosome Location	chr2:40907915-40907916
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1003618	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10177056	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178374	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178666	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10180556	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10469903	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10469904	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11124758	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1119785	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12475258	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12478853	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12619861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13016243	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1379037	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1456578	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1456581	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1456582	1.00[ASN][1000 genomes]
rs1456583	1.00[ASN][1000 genomes]
rs1456588	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1456589	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1468799	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs173799	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs173802	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs173803	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs173805	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1840756	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1861308	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1990618	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2019379	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2019768	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2077825	0.85[ASN][1000 genomes]
rs2192821	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2216035	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2216040	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2216042	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2373898	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2373904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2373936	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3922281	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs42784	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4539838	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952636	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4952642	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6544354	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6709044	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6709173	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6713163	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6728651	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6743662	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6750481	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6753289	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67806170	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7369131	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7556714	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs756376	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7564682	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7587020	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7588298	0.96[AMR][1000 genomes]
rs7591373	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591414	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7596941	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7605586	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9309059	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv873917	chr2:40710953-41015998	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv528865	chr2:40805427-41218810	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv873924	chr2:40835285-40926138	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
5	nsv873925	chr2:40835285-40966719	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
6	nsv873926	chr2:40835285-40986860	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv873927	chr2:40835285-41034225	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv470455	chr2:40835285-41059164	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv873928	chr2:40835285-41075134	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv873929	chr2:40835285-41180690	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv873931	chr2:40869165-40966719	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
12	nsv873932	chr2:40880043-40912597	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
13	nsv456441	chr2:40882402-41064824	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv581514	chr2:40882402-41064824	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv456452	chr2:40890416-40989061	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv581515	chr2:40890416-40989061	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs993867	TGIF2LX	trans	lymphoblastoid	seeQTL
rs993867	ALDH1A3	trans	lymphoblastoid	seeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40905400-40917200	Weak transcription	Aorta	Aorta
2	chr2:40907000-40908000	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr2:40907000-40908000	Active TSS	NHLF	lung
4	chr2:40907000-40908200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:40907000-40908200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:40907200-40908000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:40907200-40908000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:40907200-40908000	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr2:40907200-40908000	Active TSS	Right Atrium	heart
10	chr2:40907200-40908000	Active TSS	Monocytes-CD14+_RO01746	blood
11	chr2:40907200-40908000	Active TSS	NHDF-Ad	bronchial
12	chr2:40907400-40908000	Active TSS	Colon Smooth Muscle	Colon
13	chr2:40907400-40908000	Active TSS	Ovary	ovary
14	chr2:40907400-40908200	Active TSS	Primary monocytes fromperipheralblood	blood
15	chr2:40907600-40908000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:40907600-40908000	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr2:40907600-40908000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:40907600-40908000	Flanking Active TSS	Rectal Smooth Muscle	rectum
19	chr2:40907600-40908000	Active TSS	Stomach Smooth Muscle	stomach
20	chr2:40907600-40908000	Flanking Active TSS	Dnd41	blood
21	chr2:40907600-40908000	Active TSS	GM12878-XiMat	blood
22	chr2:40907600-40908200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:40907800-40908000	Active TSS	Adipose Nuclei	Adipose
24	chr2:40907800-40908000	Active TSS	Osteobl	bone

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