Variant report

Variant	rs2542578
Chromosome Location	chr2:54049711-54049712
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11897282	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11901698	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1232	0.89[ASN][1000 genomes]
rs13408029	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17045176	0.83[ASN][1000 genomes]
rs17045203	0.80[ASN][1000 genomes]
rs17520505	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17521008	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2008082	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2302797	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2542572	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2542573	0.87[ASN][1000 genomes]
rs2542580	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2542581	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2542589	0.83[ASN][1000 genomes]
rs2542590	0.83[ASN][1000 genomes]
rs2542591	0.83[ASN][1000 genomes]
rs2542592	0.90[ASN][1000 genomes]
rs2543629	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2692512	0.86[ASN][1000 genomes]
rs2692513	0.86[ASN][1000 genomes]
rs2692519	0.86[ASN][1000 genomes]
rs2692521	0.90[ASN][1000 genomes]
rs2692522	0.84[ASN][1000 genomes]
rs2692523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2692535	0.93[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2949813	0.93[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2949814	0.86[ASN][1000 genomes]
rs35772199	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3770394	0.85[ASN][1000 genomes]
rs3770395	0.85[ASN][1000 genomes]
rs3770397	0.83[ASN][1000 genomes]
rs3770399	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3922262	0.84[AFR][1000 genomes]
rs4116709	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56214822	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56228834	0.82[AFR][1000 genomes]
rs62137565	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62137573	0.91[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs62137602	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62137606	0.85[ASN][1000 genomes]
rs62137611	0.82[AFR][1000 genomes]
rs62137612	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6730006	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs719127	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72901256	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7558968	0.90[AMR][1000 genomes];0.90[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	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[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:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54015200-54051600	Weak transcription	Stomach Mucosa	stomach
2	chr2:54015200-54053800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:54015600-54054600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:54015800-54054000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:54023000-54053800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:54025800-54062000	Weak transcription	Right Ventricle	heart
7	chr2:54025800-54085600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:54030400-54063000	Weak transcription	Esophagus	oesophagus
9	chr2:54035800-54052800	Weak transcription	Brain Substantia Nigra	brain
10	chr2:54038800-54053000	Weak transcription	Fetal Brain Male	brain
11	chr2:54040200-54055000	Weak transcription	Fetal Heart	heart
12	chr2:54040600-54053000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:54040800-54053000	Weak transcription	Brain Angular Gyrus	brain
14	chr2:54040800-54053000	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:54041400-54054600	Weak transcription	Psoas Muscle	Psoas
16	chr2:54041400-54056400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:54042800-54062200	Weak transcription	Fetal Kidney	kidney
18	chr2:54043000-54053800	Weak transcription	NHEK	skin
19	chr2:54043200-54053000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:54043200-54053800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:54043400-54053000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:54043400-54053600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:54045400-54053000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr2:54045400-54053000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr2:54046000-54053600	Weak transcription	NH-A	brain
26	chr2:54046200-54050200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:54046200-54050600	Strong transcription	Fetal Stomach	stomach
28	chr2:54046400-54053000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:54046600-54049800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr2:54046600-54080200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr2:54046600-54080200	Weak transcription	NHDF-Ad	bronchial
32	chr2:54046800-54053000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:54046800-54054000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr2:54046800-54054200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:54046800-54054200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr2:54046800-54056800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr2:54046800-54060400	Weak transcription	Primary B cells from cord blood	blood
38	chr2:54046800-54070800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:54046800-54080400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr2:54047000-54051200	Weak transcription	HUVEC	blood vessel
41	chr2:54047000-54053000	Weak transcription	Ovary	ovary
42	chr2:54047000-54053000	Weak transcription	HMEC	breast
43	chr2:54047000-54053800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:54047000-54054000	Weak transcription	NHLF	lung
45	chr2:54047000-54056600	Weak transcription	Brain Germinal Matrix	brain
46	chr2:54047000-54060600	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr2:54047000-54061400	Weak transcription	Fetal Thymus	thymus
48	chr2:54047000-54080200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr2:54047000-54080200	Weak transcription	A549	lung
50	chr2:54047000-54080400	Weak transcription	Gastric	stomach

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