Variant report

Variant	rs6545403
Chromosome Location	chr2:54630402-54630403
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54569839..54572791-chr2:54629016..54630836,2	K562	blood:
2	chr2:54628611..54630630-chr2:54636433..54637977,2	K562	blood:
3	chr2:54629237..54631678-chr2:54647068..54649301,2	K562	blood:
4	chr2:54629042..54631678-chr2:54646319..54649301,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10198148	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10198625	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10203844	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10779939	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10865283	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11125534	0.83[ASN][1000 genomes]
rs11125538	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11674998	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12713257	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392262	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34748765	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3951717	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233947	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4233948	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4233949	0.83[ASN][1000 genomes]
rs4315567	0.94[ASN][1000 genomes]
rs4359699	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4417755	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4439997	0.88[ASN][1000 genomes]
rs4450644	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4588223	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671213	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671214	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671215	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671923	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671924	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671925	0.83[ASN][1000 genomes]
rs4671926	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671928	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545401	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6710292	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6718253	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6734097	0.94[ASN][1000 genomes]
rs6748228	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6752877	0.94[ASN][1000 genomes]
rs6760027	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7565489	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7576075	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7592359	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7592641	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595929	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7597837	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7601198	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7605902	0.83[ASN][1000 genomes]
rs7607093	0.94[ASN][1000 genomes]
rs8179723	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9677336	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9677338	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9677960	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9679192	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv532512	chr2:54453210-54630755	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54615400-54643000	Weak transcription	Right Ventricle	heart
2	chr2:54618600-54647200	Weak transcription	Left Ventricle	heart
3	chr2:54623600-54643000	Weak transcription	Lung	lung
4	chr2:54626000-54630600	Weak transcription	Brain Substantia Nigra	brain
5	chr2:54627800-54630800	Enhancers	Ovary	ovary
6	chr2:54628000-54631200	Enhancers	NHLF	lung
7	chr2:54628200-54630800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr2:54628400-54630600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:54628400-54630600	Enhancers	Fetal Lung	lung
10	chr2:54629000-54631200	Enhancers	NHDF-Ad	bronchial
11	chr2:54629200-54630600	Enhancers	Fetal Muscle Leg	muscle
12	chr2:54629200-54630600	Enhancers	Osteobl	bone
13	chr2:54629400-54630600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:54629400-54630600	Enhancers	Spleen	Spleen
15	chr2:54629600-54630800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:54629600-54631200	Enhancers	Brain Cingulate Gyrus	brain
17	chr2:54629600-54631800	Enhancers	Brain Hippocampus Middle	brain
18	chr2:54629800-54630600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:54630000-54630800	Bivalent Enhancer	HepG2	liver
20	chr2:54630000-54631000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:54630000-54634200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:54630000-54634800	Weak transcription	HSMMtube	muscle
23	chr2:54630000-54638800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:54630200-54630800	Enhancers	Brain Anterior Caudate	brain
25	chr2:54630200-54630800	Enhancers	Fetal Heart	heart
26	chr2:54630200-54631200	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr2:54630200-54631200	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr2:54630200-54637000	Weak transcription	Fetal Stomach	stomach
29	chr2:54630400-54630600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:54630400-54630800	Enhancers	Brain Angular Gyrus	brain
31	chr2:54630400-54631200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links