Variant report

Variant	rs13025954
Chromosome Location	chr2:152585020-152585021
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10169098	0.90[CEU][hapmap]
rs10172958	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs10173335	0.80[CEU][hapmap]
rs10173570	0.82[AMR][1000 genomes]
rs10174624	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10186879	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10192459	0.80[CEU][hapmap]
rs10198509	0.82[AMR][1000 genomes]
rs10202662	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10204195	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10210114	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10497093	0.90[CEU][hapmap]
rs11692567	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11885813	0.80[CEU][hapmap]
rs12328396	1.00[CEU][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12693088	0.80[CEU][hapmap];0.82[YRI][hapmap]
rs12992632	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs12994595	1.00[CEU][hapmap]
rs13384856	1.00[CEU][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13396377	0.91[EUR][1000 genomes]
rs13402710	0.86[CEU][hapmap]
rs13408513	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13414130	0.82[AMR][1000 genomes]
rs13416266	0.82[AMR][1000 genomes]
rs13421183	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13427102	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16830358	0.82[AMR][1000 genomes]
rs2030589	0.90[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap]
rs36111287	0.82[AMR][1000 genomes]
rs36141926	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3768656	0.90[CEU][hapmap]
rs4436952	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4503987	1.00[CEU][hapmap];0.85[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4525690	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6433628	0.82[AMR][1000 genomes]
rs6729878	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs6750638	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6754783	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7560854	1.00[CEU][hapmap]
rs7565109	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7591340	0.82[AMR][1000 genomes]
rs7591363	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];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	nsv934136	chr2:152308156-152664443	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv933357	chr2:152526786-152591138	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152581800-152585400	Weak transcription	Psoas Muscle	Psoas
2	chr2:152582800-152586400	Strong transcription	Fetal Muscle Trunk	muscle
3	chr2:152583000-152586400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
4	chr2:152583000-152587400	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
5	chr2:152584000-152585200	Flanking Active TSS	A549	lung
6	chr2:152584000-152588400	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr2:152584000-152588600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr2:152584000-152591000	Enhancers	Fetal Lung	lung
9	chr2:152584200-152585200	Enhancers	HepG2	liver
10	chr2:152584200-152585600	Enhancers	Stomach Mucosa	stomach
11	chr2:152584200-152587000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr2:152584200-152588200	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr2:152584200-152588200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr2:152584200-152588400	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr2:152584400-152585200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:152584400-152585600	Strong transcription	Fetal Muscle Leg	muscle
17	chr2:152584400-152585800	Weak transcription	HSMMtube	muscle
18	chr2:152584600-152585200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr2:152584600-152585400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:152584600-152585600	Weak transcription	Pancreas	Pancrea
21	chr2:152584600-152588000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:152584600-152588400	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr2:152584800-152586200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:152584800-152588200	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr2:152584800-152610400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr2:152585000-152587600	Enhancers	Primary B cells from peripheral blood	blood
27	chr2:152585000-152588000	Enhancers	Primary B cells from cord blood	blood

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