Variant report

Variant	rs12914634
Chromosome Location	chr15:51413325-51413326
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10744956	0.82[CHB][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs1075681	0.94[CEU][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs10851494	0.82[JPT][hapmap]
rs11070824	0.82[CHB][hapmap]
rs11070835	0.94[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1111266	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11853672	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11854175	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11856156	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857810	0.81[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.85[MKK][hapmap];0.83[ASN][1000 genomes]
rs12101410	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902197	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12902208	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12903928	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12904382	0.81[CHB][hapmap]
rs1472946	0.82[CHB][hapmap]
rs1550336	0.81[CHB][hapmap]
rs17703090	0.82[CHB][hapmap]
rs17703599	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2118784	0.83[ASN][1000 genomes]
rs2165028	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2306335	0.95[MEX][hapmap];0.83[TSI][hapmap]
rs28408575	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28597847	0.82[ASN][1000 genomes]
rs34316637	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35044181	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35094349	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35346248	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35514320	0.87[ASN][1000 genomes]
rs35935681	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3743045	0.81[CHB][hapmap]
rs4775910	0.82[CHB][hapmap]
rs4775913	0.80[EUR][1000 genomes]
rs4775916	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55939501	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56115630	0.84[EUR][1000 genomes]
rs57428998	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57817780	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59840894	0.87[ASN][1000 genomes]
rs60981675	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6493472	0.81[EUR][1000 genomes]
rs6493476	0.81[CHB][hapmap]
rs67145268	0.85[EUR][1000 genomes]
rs67228714	0.81[EUR][1000 genomes]
rs67594971	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs68033275	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs714784	0.81[CHB][hapmap]
rs7171847	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7171946	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7183678	0.86[EUR][1000 genomes]
rs73408568	0.87[EUR][1000 genomes]
rs8025456	0.85[EUR][1000 genomes]
rs8025809	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8032051	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv904214	chr15:51204364-51535192	Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1049644	chr15:51265447-51560445	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv428634	chr15:51299632-51446666	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12914634	TMOD2	cis	cerebellum	SCAN
rs12914634	TNFAIP8L3	cis	parietal	SCAN
rs12914634	SLC30A4	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51406800-51417200	Weak transcription	Aorta	Aorta
2	chr15:51411400-51414800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr15:51412200-51413800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr15:51412600-51413400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:51412800-51414000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr15:51412800-51414200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:51412800-51414200	Enhancers	NHDF-Ad	bronchial
8	chr15:51412800-51414200	Enhancers	NHLF	lung
9	chr15:51412800-51414400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr15:51412800-51414400	Enhancers	HMEC	breast
11	chr15:51412800-51414400	Enhancers	HSMM	muscle
12	chr15:51412800-51414400	Enhancers	Osteobl	bone
13	chr15:51413000-51413400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr15:51413000-51413400	Flanking Active TSS	HUVEC	blood vessel
15	chr15:51413000-51413600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:51413000-51413600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:51413000-51413600	Enhancers	Esophagus	oesophagus
18	chr15:51413000-51413600	Enhancers	Ovary	ovary
19	chr15:51413000-51413600	Enhancers	Hela-S3	cervix
20	chr15:51413000-51413800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:51413000-51413800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:51413000-51413800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr15:51413000-51413800	Enhancers	A549	lung
24	chr15:51413000-51413800	Enhancers	HSMMtube	muscle
25	chr15:51413000-51413800	Enhancers	K562	blood
26	chr15:51413000-51413800	Enhancers	NHEK	skin
27	chr15:51413200-51413400	Flanking Active TSS	NH-A	brain
28	chr15:51413200-51413600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:51413200-51413800	Enhancers	Monocytes-CD14+_RO01746	blood

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