Variant report

Variant	rs2615127
Chromosome Location	chr16:82868138-82868139
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10781995	1.00[JPT][hapmap]
rs11150496	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs11150498	0.94[ASN][1000 genomes]
rs11150500	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11150502	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11150507	0.85[ASN][1000 genomes]
rs11641036	0.94[ASN][1000 genomes]
rs12149890	0.94[ASN][1000 genomes]
rs12918477	0.93[ASN][1000 genomes]
rs12929586	0.94[ASN][1000 genomes]
rs1381500	0.94[ASN][1000 genomes]
rs1462051	0.90[ASN][1000 genomes]
rs1559312	0.86[JPT][hapmap]
rs1585533	0.94[ASN][1000 genomes]
rs1903618	0.94[ASN][1000 genomes]
rs192598	0.86[CEU][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs192599	0.86[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1947715	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs1991024	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1991025	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2059230	0.81[GIH][hapmap];0.88[JPT][hapmap]
rs2061629	0.89[JPT][hapmap]
rs2113137	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2113138	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2113139	0.85[ASN][1000 genomes]
rs2113140	1.00[JPT][hapmap]
rs2194283	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2194285	0.82[CEU][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2325690	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2549141	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2615128	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2615133	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs286666	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286667	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286668	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286674	0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs286676	0.86[CEU][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs286678	0.86[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs286680	0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs286682	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs286684	0.86[AMR][1000 genomes]
rs286685	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs286687	0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34211526	0.83[ASN][1000 genomes]
rs3911751	0.94[ASN][1000 genomes]
rs4513093	0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4782734	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4782736	0.87[GIH][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs4783290	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4783291	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4783293	0.80[MEX][hapmap]
rs7184056	0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7198913	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7201088	0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7498269	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8051136	0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8052008	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8053647	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs918659	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs929846	0.88[JPT][hapmap]
rs929847	0.88[JPT][hapmap]
rs929848	0.88[JPT][hapmap]
rs9319576	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9319577	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9921828	0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[ASN][1000 genomes]
rs9921848	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9931196	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9933586	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9933935	0.81[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9935163	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532599	chr16:82074439-82926863	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	nsv573367	chr16:82140561-83040846	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1057341	chr16:82363800-83198907	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
4	nsv542997	chr16:82363800-83198907	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv573379	chr16:82713551-82887631	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1063617	chr16:82786803-83229529	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv907027	chr16:82830121-82871350	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv2830385	chr16:82841335-82950413	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2615127	VAT1L	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:82833000-82873600	Weak transcription	HMEC	breast
2	chr16:82848200-82898200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr16:82851000-82869200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr16:82856800-82876200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr16:82857000-82868800	Weak transcription	NHEK	skin
6	chr16:82858400-82869000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr16:82863200-82892800	Weak transcription	HSMMtube	muscle
8	chr16:82864000-82869800	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr16:82864800-82868200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr16:82865000-82870200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr16:82865200-82868200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr16:82865400-82869200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr16:82866000-82868400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr16:82866000-82868400	Enhancers	HSMM	muscle
15	chr16:82866200-82869400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr16:82866200-82869600	Enhancers	NH-A	brain
17	chr16:82866400-82869400	Enhancers	H1 Cell Line	embryonic stem cell
18	chr16:82866600-82869600	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr16:82866600-82869600	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr16:82866600-82869800	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr16:82866800-82869200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr16:82866800-82869600	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr16:82866800-82869800	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr16:82866800-82878600	Weak transcription	Aorta	Aorta
25	chr16:82867000-82868200	Enhancers	H9 Cell Line	embryonic stem cell
26	chr16:82867000-82868400	Enhancers	Left Ventricle	heart
27	chr16:82867000-82869400	Enhancers	Right Ventricle	heart
28	chr16:82867000-82869600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr16:82867200-82869800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr16:82867200-82870200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr16:82867400-82868200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr16:82867400-82868600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr16:82867400-82868800	Weak transcription	Fetal Muscle Leg	muscle
34	chr16:82867400-82872200	Weak transcription	Psoas Muscle	Psoas
35	chr16:82867400-82874600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr16:82867600-82869000	Weak transcription	NHDF-Ad	bronchial
37	chr16:82868000-82868200	Enhancers	Fetal Muscle Trunk	muscle
38	chr16:82868000-82868400	Enhancers	Right Atrium	heart
39	chr16:82868000-82869200	Weak transcription	Osteobl	bone

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