Variant report

Variant	rs2540228
Chromosome Location	chr2:39954632-39954633
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10164984	0.80[EUR][1000 genomes]
rs10174709	0.89[EUR][1000 genomes]
rs10206408	0.81[EUR][1000 genomes]
rs10207589	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10211306	0.86[EUR][1000 genomes]
rs11124691	0.82[EUR][1000 genomes]
rs11124692	0.82[ASN][1000 genomes]
rs11124693	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11684302	0.81[CEU][hapmap]
rs12470473	0.84[CEU][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.87[EUR][1000 genomes]
rs12623545	0.82[EUR][1000 genomes]
rs12624217	0.81[CEU][hapmap]
rs12712656	0.90[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs13026313	0.85[CEU][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs13428837	0.80[EUR][1000 genomes]
rs1548877	0.89[EUR][1000 genomes]
rs17478972	0.80[CEU][hapmap];0.90[CHB][hapmap];0.80[EUR][1000 genomes]
rs1861243	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1861258	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs2041735	0.86[EUR][1000 genomes]
rs2058620	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs2110656	0.80[ASW][hapmap];0.88[CEU][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2160199	0.85[ASW][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2192685	0.90[CHB][hapmap];0.91[CHD][hapmap];0.81[ASN][1000 genomes]
rs2192686	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2215958	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2241115	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2373689	0.84[CEU][hapmap];0.80[GIH][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs2540226	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2540227	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2540229	0.82[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2716681	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2716699	0.82[AMR][1000 genomes]
rs2716729	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2716730	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs3732121	0.83[EUR][1000 genomes]
rs3732122	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs3815510	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs4670956	0.92[CEU][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4670957	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs4670958	0.84[CEU][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4670959	0.81[CEU][hapmap]
rs59756273	0.85[EUR][1000 genomes]
rs6544242	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6722610	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6731026	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6731450	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6747842	0.83[JPT][hapmap]
rs7560642	0.88[CEU][hapmap];0.85[GIH][hapmap];0.89[EUR][1000 genomes]
rs7581406	0.82[EUR][1000 genomes]
rs7590912	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7591296	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7591347	0.98[EUR][1000 genomes]
rs8265	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs917961	0.85[ASW][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.93[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs917962	0.92[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs917963	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs962262	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs997976	0.85[CEU][hapmap];0.85[GIH][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2540228	THUMPD2	cis	cerebellum	SCAN
rs2540228	THUMPD2	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39925000-39957600	Weak transcription	Fetal Stomach	stomach
2	chr2:39931400-39957600	Weak transcription	Fetal Muscle Leg	muscle
3	chr2:39938000-39957600	Weak transcription	Fetal Brain Female	brain
4	chr2:39942000-39963000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr2:39943200-39956200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:39944400-39976600	Weak transcription	Fetal Brain Male	brain
7	chr2:39946800-39959600	Weak transcription	Brain Germinal Matrix	brain
8	chr2:39947800-39959800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:39948200-39961200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr2:39948800-39959600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:39949000-39960400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr2:39951000-39956000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:39951000-39957400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:39951000-39959400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:39951000-39963600	Weak transcription	Pancreas	Pancrea
16	chr2:39951000-39964800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:39951200-39957600	Weak transcription	Fetal Lung	lung
18	chr2:39951200-39964800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:39951400-39957800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr2:39951400-39958800	Weak transcription	Aorta	Aorta
21	chr2:39951400-39960200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:39951400-39961400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:39951400-39961800	Weak transcription	Colon Smooth Muscle	Colon
24	chr2:39951400-39962000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr2:39951400-39963800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr2:39952000-39956200	Weak transcription	Psoas Muscle	Psoas
27	chr2:39952000-39964800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:39952200-39957400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:39952200-39960200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:39952400-39955400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:39952400-39957400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:39952400-39958800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:39952400-39962400	Weak transcription	Spleen	Spleen
34	chr2:39952600-39962600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:39952800-39955400	Weak transcription	HSMM	muscle
36	chr2:39952800-39957600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:39952800-39960200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:39952800-39962400	Weak transcription	Fetal Kidney	kidney
39	chr2:39952800-39962600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:39953000-39957800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:39953000-39959400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:39953200-39957800	Weak transcription	Osteobl	bone
43	chr2:39953200-39958800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:39953200-39962400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr2:39953400-39955600	Weak transcription	NH-A	brain
46	chr2:39953600-39959000	Weak transcription	HMEC	breast
47	chr2:39953600-39959400	Weak transcription	Esophagus	oesophagus
48	chr2:39953800-39955400	Weak transcription	GM12878-XiMat	blood
49	chr2:39953800-39958600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:39954000-39958800	Weak transcription	Left Ventricle	heart

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