Variant report

Variant	rs2542580
Chromosome Location	chr2:54051744-54051745
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10490468	0.84[ASN][1000 genomes]
rs11897282	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11901698	0.86[EUR][1000 genomes]
rs1232	0.89[ASN][1000 genomes]
rs13408029	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17045176	0.88[ASN][1000 genomes]
rs17045203	0.81[ASN][1000 genomes]
rs17520505	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17521008	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2008082	0.86[EUR][1000 genomes]
rs2287340	0.82[ASN][1000 genomes]
rs2302797	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2542572	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2542573	0.92[ASN][1000 genomes]
rs2542578	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2542581	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2542582	0.80[ASN][1000 genomes]
rs2542589	0.88[ASN][1000 genomes]
rs2542590	0.88[ASN][1000 genomes]
rs2542591	0.88[ASN][1000 genomes]
rs2542592	0.90[ASN][1000 genomes]
rs2543629	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2692512	0.92[ASN][1000 genomes]
rs2692513	0.92[ASN][1000 genomes]
rs2692519	0.86[ASN][1000 genomes]
rs2692521	0.90[ASN][1000 genomes]
rs2692522	0.89[ASN][1000 genomes]
rs2692523	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2692535	0.81[ASN][1000 genomes]
rs2949813	0.92[ASN][1000 genomes]
rs2949814	0.86[ASN][1000 genomes]
rs35772199	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3770394	0.85[ASN][1000 genomes]
rs3770395	0.85[ASN][1000 genomes]
rs3770397	0.88[ASN][1000 genomes]
rs3770399	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4116709	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56214822	0.86[EUR][1000 genomes]
rs62137565	0.86[EUR][1000 genomes]
rs62137573	0.84[ASN][1000 genomes]
rs62137602	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62137606	0.85[ASN][1000 genomes]
rs62137610	0.81[ASN][1000 genomes]
rs62137611	0.81[ASN][1000 genomes]
rs62137612	0.81[ASN][1000 genomes]
rs6730006	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs719127	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72901256	0.86[ASN][1000 genomes]
rs7558968	0.86[EUR][1000 genomes]
rs7600817	0.85[ASN][1000 genomes]
rs805368	0.87[ASN][1000 genomes]
rs805383	0.89[ASN][1000 genomes]
rs805385	0.89[ASN][1000 genomes]
rs805398	0.85[ASN][1000 genomes]
rs805413	0.82[ASN][1000 genomes]
rs805435	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs805437	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS 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	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54015200-54053800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:54015600-54054600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:54015800-54054000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:54023000-54053800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:54025800-54062000	Weak transcription	Right Ventricle	heart
6	chr2:54025800-54085600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:54030400-54063000	Weak transcription	Esophagus	oesophagus
8	chr2:54035800-54052800	Weak transcription	Brain Substantia Nigra	brain
9	chr2:54038800-54053000	Weak transcription	Fetal Brain Male	brain
10	chr2:54040200-54055000	Weak transcription	Fetal Heart	heart
11	chr2:54040600-54053000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:54040800-54053000	Weak transcription	Brain Angular Gyrus	brain
13	chr2:54040800-54053000	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:54041400-54054600	Weak transcription	Psoas Muscle	Psoas
15	chr2:54041400-54056400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr2:54042800-54062200	Weak transcription	Fetal Kidney	kidney
17	chr2:54043000-54053800	Weak transcription	NHEK	skin
18	chr2:54043200-54053000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:54043200-54053800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:54043400-54053000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:54043400-54053600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr2:54045400-54053000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr2:54045400-54053000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:54046000-54053600	Weak transcription	NH-A	brain
25	chr2:54046400-54053000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr2:54046600-54080200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr2:54046600-54080200	Weak transcription	NHDF-Ad	bronchial
28	chr2:54046800-54053000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:54046800-54054000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr2:54046800-54054200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:54046800-54054200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:54046800-54056800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr2:54046800-54060400	Weak transcription	Primary B cells from cord blood	blood
34	chr2:54046800-54070800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:54046800-54080400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr2:54047000-54053000	Weak transcription	Ovary	ovary
37	chr2:54047000-54053000	Weak transcription	HMEC	breast
38	chr2:54047000-54053800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:54047000-54054000	Weak transcription	NHLF	lung
40	chr2:54047000-54056600	Weak transcription	Brain Germinal Matrix	brain
41	chr2:54047000-54060600	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr2:54047000-54061400	Weak transcription	Fetal Thymus	thymus
43	chr2:54047000-54080200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:54047000-54080200	Weak transcription	A549	lung
45	chr2:54047000-54080400	Weak transcription	Gastric	stomach
46	chr2:54047000-54080400	Weak transcription	Pancreas	Pancrea
47	chr2:54047000-54080800	Weak transcription	Aorta	Aorta
48	chr2:54047200-54052400	Weak transcription	Liver	Liver
49	chr2:54047200-54052400	Weak transcription	Brain Anterior Caudate	brain
50	chr2:54047200-54052400	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links