Variant report

Variant	rs2000141
Chromosome Location	chr1:56756491-56756492
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10888961	0.80[EUR][1000 genomes]
rs11206765	0.84[EUR][1000 genomes]
rs12075857	0.84[EUR][1000 genomes]
rs12075995	0.84[EUR][1000 genomes]
rs12076123	0.84[EUR][1000 genomes]
rs12077346	0.84[EUR][1000 genomes]
rs12077564	0.84[EUR][1000 genomes]
rs12081440	0.84[EUR][1000 genomes]
rs12082680	0.84[EUR][1000 genomes]
rs12562857	0.80[EUR][1000 genomes]
rs12565829	0.80[EUR][1000 genomes]
rs12567619	0.84[EUR][1000 genomes]
rs17113677	0.81[AFR][1000 genomes]
rs17113689	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17424500	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17424899	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17425099	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17425772	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17458279	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17459027	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2000142	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2153667	0.81[EUR][1000 genomes]
rs2404528	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3992066	0.81[EUR][1000 genomes]
rs55633488	0.84[EUR][1000 genomes]
rs55652225	0.81[EUR][1000 genomes]
rs55742346	0.84[EUR][1000 genomes]
rs56022955	0.84[EUR][1000 genomes]
rs56237067	0.84[EUR][1000 genomes]
rs61379230	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72660403	0.81[EUR][1000 genomes]
rs72660452	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72660457	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72677472	0.83[EUR][1000 genomes]
rs72677474	0.81[EUR][1000 genomes]
rs72677478	0.81[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	nsv1006422	chr1:56734772-56828606	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv534972	chr1:56734772-56828606	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2000141	MYSM1	cis	cerebellum	SCAN
rs2000141	CC2D1B	cis	parietal	SCAN
rs2000141	CDCP2	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56745400-56757000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:56748400-56759600	Weak transcription	Aorta	Aorta
3	chr1:56751400-56756800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:56751400-56757600	Weak transcription	Pancreas	Pancrea
5	chr1:56751800-56756800	Weak transcription	Lung	lung
6	chr1:56752000-56756800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:56752000-56757000	Weak transcription	Fetal Stomach	stomach
8	chr1:56752000-56757000	Weak transcription	HSMMtube	muscle
9	chr1:56752600-56756800	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:56752800-56756800	Weak transcription	Adipose Nuclei	Adipose
11	chr1:56752800-56756800	Weak transcription	Psoas Muscle	Psoas
12	chr1:56752800-56756800	Weak transcription	Right Atrium	heart
13	chr1:56752800-56756800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:56753200-56756800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:56753200-56763600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:56753400-56756800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:56753600-56756800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:56753600-56756800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr1:56753600-56756800	Weak transcription	Placenta	Placenta
20	chr1:56753600-56757000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:56755200-56756800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:56755400-56756800	Weak transcription	Left Ventricle	heart
23	chr1:56755800-56757600	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr1:56755800-56757800	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr1:56756000-56757000	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr1:56756000-56757400	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr1:56756000-56757800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:56756000-56758000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:56756000-56761800	Weak transcription	HepG2	liver
30	chr1:56756200-56757000	Enhancers	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links