Variant report

Variant	rs2782540
Chromosome Location	chr1:61776141-61776142
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1041674	0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10489912	0.81[MKK][hapmap]
rs1125777	0.81[JPT][hapmap]
rs1414265	0.85[CHB][hapmap];0.84[LWK][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap]
rs2024789	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2782543	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2782547	0.85[CHB][hapmap]
rs2806435	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2806437	0.98[ASN][1000 genomes]
rs2806442	1.00[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2970457	0.85[CHB][hapmap]
rs41350144	0.86[JPT][hapmap]
rs6670529	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6691768	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6696260	0.82[MEX][hapmap]
rs7521242	0.85[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv994970	chr1:61693951-62199657	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1006142	chr1:61696142-62119763	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised 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
3	nsv534980	chr1:61696142-62119763	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised 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
4	nsv916868	chr1:61700430-62119762	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised 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
5	nsv1001052	chr1:61702011-62090670	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv817402	chr1:61703965-62119762	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1010797	chr1:61703966-62125970	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv530494	chr1:61723918-62084045	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS 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	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2782540	DLEU2L	cis	cerebellum	SCAN
rs2782540	MYSM1	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:61744600-61798600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr1:61755600-61784000	Weak transcription	Esophagus	oesophagus
3	chr1:61760800-61780800	Weak transcription	Fetal Brain Male	brain
4	chr1:61760800-61783800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:61765400-61779200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:61765400-61779400	Weak transcription	HUVEC	blood vessel
7	chr1:61765400-61784000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:61765600-61777600	Weak transcription	Fetal Intestine Small	intestine
9	chr1:61767800-61779000	Weak transcription	Pancreas	Pancrea
10	chr1:61767800-61782200	Weak transcription	Lung	lung
11	chr1:61767800-61783800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:61767800-61784000	Weak transcription	Liver	Liver
13	chr1:61768000-61778800	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:61768000-61782000	Weak transcription	Ovary	ovary
15	chr1:61768000-61783600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:61768000-61783800	Weak transcription	Colon Smooth Muscle	Colon
17	chr1:61768000-61783800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:61768000-61784400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:61768200-61781000	Weak transcription	Brain Substantia Nigra	brain
20	chr1:61768400-61778800	Weak transcription	Fetal Lung	lung
21	chr1:61768400-61780800	Weak transcription	Fetal Heart	heart
22	chr1:61768400-61781600	Weak transcription	Fetal Stomach	stomach
23	chr1:61768600-61782200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:61768800-61782000	Weak transcription	Adipose Nuclei	Adipose
25	chr1:61768800-61784400	Weak transcription	A549	lung
26	chr1:61769200-61782000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:61769400-61779200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:61769400-61783600	Weak transcription	NHEK	skin
29	chr1:61769400-61784000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:61773200-61781600	Weak transcription	Psoas Muscle	Psoas
31	chr1:61773400-61783400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:61774000-61779000	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr1:61774200-61783400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:61774800-61778800	Weak transcription	Fetal Intestine Large	intestine
35	chr1:61775400-61776400	Enhancers	K562	blood
36	chr1:61775800-61776600	Strong transcription	Aorta	Aorta
37	chr1:61775800-61778200	Strong transcription	HepG2	liver
38	chr1:61776000-61776200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:61776000-61776200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr1:61776000-61776200	Enhancers	Right Ventricle	heart
41	chr1:61776000-61776600	Enhancers	Right Atrium	heart
42	chr1:61776000-61776800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:61776000-61778000	Enhancers	Left Ventricle	heart
44	chr1:61776000-61778400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:61776000-61784600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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