Variant report

Variant	rs2125094
Chromosome Location	chr12:10730745-10730746
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 104 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10734838	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10743910	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10772315	0.83[ASN][1000 genomes]
rs10772316	0.85[ASN][1000 genomes]
rs10772317	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10772318	0.92[ASN][1000 genomes]
rs10772319	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10772321	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10772323	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10772324	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10772325	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10772326	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10772327	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10772329	0.82[ASN][1000 genomes]
rs10845153	0.87[CHB][hapmap]
rs10845161	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs10845162	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10845163	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845164	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845165	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10845166	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10845172	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845174	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10845175	0.90[CHD][hapmap];0.85[JPT][hapmap]
rs11053857	0.81[ASN][1000 genomes]
rs11053859	0.85[ASN][1000 genomes]
rs11053865	0.83[ASN][1000 genomes]
rs11053869	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11053870	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11053871	0.83[ASN][1000 genomes]
rs11053873	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11053874	0.89[JPT][hapmap]
rs11611202	0.85[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs12423957	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1915322	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1915323	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2002156	0.83[ASN][1000 genomes]
rs2002157	0.81[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2125092	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2125095	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2168750	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2417745	0.95[JPT][hapmap]
rs2417746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2417747	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2417748	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2417900	0.84[CHB][hapmap]
rs2417901	0.84[CHB][hapmap]
rs2607883	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2607888	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2607891	0.95[JPT][hapmap]
rs2607892	0.95[JPT][hapmap]
rs2607895	0.95[JPT][hapmap]
rs2607898	0.94[JPT][hapmap]
rs2682476	0.95[JPT][hapmap]
rs3816567	0.85[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs3867478	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3983544	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3983545	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3983546	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3983547	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4237928	0.84[ASN][1000 genomes]
rs4476009	0.84[ASN][1000 genomes]
rs4536307	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4763528	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763530	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4763531	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763532	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763547	0.84[ASN][1000 genomes]
rs4763548	0.84[ASN][1000 genomes]
rs4763550	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763551	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763553	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763555	0.83[ASN][1000 genomes]
rs4763556	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4763558	0.85[ASN][1000 genomes]
rs4763559	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58917785	0.83[ASN][1000 genomes]
rs60367665	0.81[ASN][1000 genomes]
rs61913124	0.81[ASN][1000 genomes]
rs6488302	0.84[CHB][hapmap]
rs6488303	0.84[CHB][hapmap]
rs6488304	0.84[CHB][hapmap]
rs6488307	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7134658	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7134908	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7136310	0.86[ASN][1000 genomes]
rs7136964	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7137465	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7306285	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7306724	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7311860	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315514	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7955358	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7955359	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7964171	0.92[ASN][1000 genomes]
rs7964203	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7965052	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978788	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7978850	0.81[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7979402	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7980411	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2125094	CLEC4E	cis	parietal	SCAN
rs2125094	CLEC12B	cis	cerebellum	SCAN
rs2125094	KLRA1	cis	cerebellum	SCAN
rs2125094	NOP2	cis	cerebellum	SCAN

Chromatin state (count:31 , 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	chr12:10725800-10732600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr12:10725800-10732600	Weak transcription	A549	lung
11	chr12:10725800-10733000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr12:10725800-10733200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:10725800-10733800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:10725800-10743200	Weak transcription	NHDF-Ad	bronchial
15	chr12:10725800-10753400	Weak transcription	Osteobl	bone
16	chr12:10725800-10761400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:10726200-10732200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr12:10726200-10732400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr12:10726200-10734400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:10726400-10743200	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr12:10726400-10759800	Weak transcription	NHLF	lung
22	chr12:10726800-10732200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:10726800-10733200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:10726800-10756600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:10727400-10732400	Weak transcription	HSMM	muscle
26	chr12:10729200-10732400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:10729800-10733800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr12:10730000-10732400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr12:10730000-10762000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr12:10730600-10733800	Weak transcription	Liver	Liver
31	chr12:10730600-10764800	Weak transcription	Lung	lung

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