Variant report

Variant	rs2125096
Chromosome Location	chr12:10727676-10727677
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10734838	0.81[ASN][1000 genomes]
rs10743910	0.81[ASN][1000 genomes]
rs10772319	0.81[ASN][1000 genomes]
rs10772321	0.81[ASN][1000 genomes]
rs10772323	0.81[ASN][1000 genomes]
rs10772326	0.81[ASN][1000 genomes]
rs10772327	0.81[ASN][1000 genomes]
rs10845162	0.81[AFR][1000 genomes]
rs10845165	0.83[AFR][1000 genomes]
rs10845171	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845172	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10845173	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11053860	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11053861	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11053868	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11053869	0.81[ASN][1000 genomes]
rs11053870	0.81[ASN][1000 genomes]
rs11053873	0.81[AFR][1000 genomes]
rs11053874	0.94[CHB][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12312462	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1915322	0.83[AFR][1000 genomes]
rs1915323	0.81[ASN][1000 genomes]
rs2125093	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2168750	0.81[ASN][1000 genomes]
rs2417745	0.80[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2417746	0.90[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes]
rs2417748	0.83[AFR][1000 genomes]
rs2607883	0.90[JPT][hapmap]
rs2607885	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2607886	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2607887	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2607888	0.90[JPT][hapmap]
rs2607889	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2607890	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2607891	0.87[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2607892	0.87[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2607893	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2607895	0.86[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2607896	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2607898	0.84[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2682474	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2682476	0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3983544	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3983545	0.81[ASN][1000 genomes]
rs3983546	0.81[ASN][1000 genomes]
rs4076336	0.83[ASN][1000 genomes]
rs4237929	0.83[ASN][1000 genomes]
rs4763552	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763559	0.81[ASN][1000 genomes]
rs6488306	0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs6488307	0.81[ASN][1000 genomes]
rs7134658	0.81[ASN][1000 genomes]
rs7134908	0.81[ASN][1000 genomes]
rs7306285	0.81[ASN][1000 genomes]
rs7358656	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7488589	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953221	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971934	0.81[ASN][1000 genomes]
rs7980411	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv557459	chr12:10560591-10729821	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv557479	chr12:10644663-10729821	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv898775	chr12:10668694-10735786	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1039120	chr12:10675930-10755446	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv832329	chr12:10677094-10845946	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 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	chr12:10714000-10733200	Weak transcription	Primary T cells from cord blood	blood
2	chr12:10724000-10733200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:10724000-10733400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:10725000-10733600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:10725200-10732200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:10725600-10732400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:10725600-10743600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr12:10725600-10765000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:10725800-10729600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:10725800-10732600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:10725800-10732600	Weak transcription	A549	lung
12	chr12:10725800-10733000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:10725800-10733200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:10725800-10733800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:10725800-10743200	Weak transcription	NHDF-Ad	bronchial
16	chr12:10725800-10753400	Weak transcription	Osteobl	bone
17	chr12:10725800-10761400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:10726000-10729800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr12:10726200-10732200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:10726200-10732400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr12:10726200-10734400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:10726400-10743200	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr12:10726400-10759800	Weak transcription	NHLF	lung
24	chr12:10726800-10732200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:10726800-10733200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:10726800-10756600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:10727400-10732400	Weak transcription	HSMM	muscle

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