Variant report

Variant	rs6752877
Chromosome Location	chr2:54661569-54661570
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10198148	0.88[ASN][1000 genomes]
rs10198625	0.88[ASN][1000 genomes]
rs10779939	0.82[ASN][1000 genomes]
rs11125538	0.88[ASN][1000 genomes]
rs11898505	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12713257	0.94[ASN][1000 genomes]
rs13392262	0.94[ASN][1000 genomes]
rs34748765	0.88[ASN][1000 genomes]
rs3951717	0.94[ASN][1000 genomes]
rs4024576	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4233947	0.88[ASN][1000 genomes]
rs4233948	0.88[ASN][1000 genomes]
rs4233949	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4315567	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4359699	0.88[ASN][1000 genomes]
rs4439997	0.82[ASN][1000 genomes]
rs4450644	0.88[ASN][1000 genomes]
rs4588223	0.94[ASN][1000 genomes]
rs4671213	0.94[ASN][1000 genomes]
rs4671214	0.88[ASN][1000 genomes]
rs4671215	0.88[ASN][1000 genomes]
rs4671923	0.88[ASN][1000 genomes]
rs4671924	0.88[ASN][1000 genomes]
rs4671926	0.88[ASN][1000 genomes]
rs4671928	0.88[ASN][1000 genomes]
rs6545403	0.94[ASN][1000 genomes]
rs6710292	0.94[ASN][1000 genomes]
rs6718253	0.88[ASN][1000 genomes]
rs6734097	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748228	0.88[ASN][1000 genomes]
rs6760027	0.94[ASN][1000 genomes]
rs7565489	0.94[ASN][1000 genomes]
rs7576075	0.88[ASN][1000 genomes]
rs7592359	0.94[ASN][1000 genomes]
rs7592641	0.94[ASN][1000 genomes]
rs7595929	0.82[ASN][1000 genomes]
rs7597837	0.88[ASN][1000 genomes]
rs7607093	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8179723	0.88[ASN][1000 genomes]
rs9677336	0.88[ASN][1000 genomes]
rs9677338	0.88[ASN][1000 genomes]
rs9679192	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6752877	BLMH	trans	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54654000-54663200	Enhancers	Fetal Muscle Leg	muscle
2	chr2:54654000-54664200	Enhancers	Adipose Nuclei	Adipose
3	chr2:54656800-54663200	Enhancers	Fetal Lung	lung
4	chr2:54656800-54665200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:54658400-54662200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:54658400-54665400	Weak transcription	Pancreas	Pancrea
7	chr2:54658600-54664000	Weak transcription	Spleen	Spleen
8	chr2:54659800-54661600	Enhancers	Lung	lung
9	chr2:54659800-54665400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:54660000-54663000	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:54660000-54664000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:54660000-54665200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:54660200-54661600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr2:54660200-54662200	Weak transcription	Fetal Heart	heart
15	chr2:54660200-54662400	Weak transcription	Brain Anterior Caudate	brain
16	chr2:54660200-54663800	Weak transcription	Left Ventricle	heart
17	chr2:54660200-54664600	Weak transcription	Brain Angular Gyrus	brain
18	chr2:54660200-54665400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:54660200-54665400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr2:54660200-54666200	Weak transcription	Psoas Muscle	Psoas
21	chr2:54660200-54666600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr2:54660200-54668200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:54660400-54663200	Enhancers	HSMMtube	muscle
24	chr2:54660600-54661800	Weak transcription	Fetal Brain Male	brain
25	chr2:54660600-54662600	Weak transcription	Brain Hippocampus Middle	brain
26	chr2:54660600-54662600	Weak transcription	Ovary	ovary
27	chr2:54660800-54662800	Weak transcription	Fetal Stomach	stomach
28	chr2:54661000-54661600	Enhancers	Right Atrium	heart
29	chr2:54661000-54662800	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr2:54661200-54662000	Enhancers	HSMM	muscle
31	chr2:54661400-54661600	Enhancers	Right Ventricle	heart
32	chr2:54661400-54661600	Enhancers	Stomach Smooth Muscle	stomach
33	chr2:54661400-54661600	Enhancers	HUVEC	blood vessel
34	chr2:54661400-54661800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links