Variant report

Variant	rs1948380
Chromosome Location	chr12:40562906-40562907
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 119 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1031996	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10748014	0.85[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs10784359	0.95[MEX][hapmap]
rs10784370	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10784381	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10784386	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10784428	0.84[ASN][1000 genomes]
rs10878089	0.85[MEX][hapmap]
rs10878113	0.82[ASN][1000 genomes]
rs10878220	0.87[ASN][1000 genomes]
rs10878222	0.85[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs10878224	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs1117378	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11175024	0.85[MEX][hapmap]
rs11175275	0.85[EUR][1000 genomes]
rs11175326	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11175327	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11175656	0.85[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs12827541	0.87[ASN][1000 genomes]
rs1352876	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1388587	0.94[ASN][1000 genomes]
rs1388588	0.91[ASN][1000 genomes]
rs1388589	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1388590	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1388591	0.82[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs1463719	0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.94[ASN][1000 genomes]
rs1463720	0.94[ASN][1000 genomes]
rs1472118	0.95[CHB][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1482284	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1482285	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1482287	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1482288	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1491927	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491928	0.94[ASN][1000 genomes]
rs1491929	0.98[ASN][1000 genomes]
rs1491930	0.90[ASN][1000 genomes]
rs1491931	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1602578	0.84[ASN][1000 genomes]
rs1844921	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1844922	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1873611	0.93[ASN][1000 genomes]
rs1873612	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1873613	0.93[ASN][1000 genomes]
rs1905121	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2131082	0.98[ASN][1000 genomes]
rs2131083	0.98[ASN][1000 genomes]
rs2170503	0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2201143	0.98[ASN][1000 genomes]
rs2220677	0.98[ASN][1000 genomes]
rs2248928	0.82[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs2249010	0.82[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs2249017	0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs2404573	0.81[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs2638231	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2638232	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638245	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2638249	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638251	0.99[ASN][1000 genomes]
rs2638252	0.94[ASN][1000 genomes]
rs2638253	0.94[ASN][1000 genomes]
rs2638254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638257	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2638258	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2638259	0.95[ASN][1000 genomes]
rs2638260	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2638262	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2638263	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2638264	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2638266	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2638267	0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs2708449	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2708464	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708466	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708467	0.98[ASN][1000 genomes]
rs2708470	0.98[ASN][1000 genomes]
rs2708472	0.98[ASN][1000 genomes]
rs2708473	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708474	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708476	0.99[ASN][1000 genomes]
rs2708477	0.82[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs2708479	0.82[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs2708480	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708481	0.82[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs2708482	0.94[ASN][1000 genomes]
rs2708485	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708487	0.94[ASN][1000 genomes]
rs2708488	0.99[ASN][1000 genomes]
rs2708489	0.94[ASN][1000 genomes]
rs2708491	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708492	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708493	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708494	0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3812791	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4360759	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap]
rs4363681	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4767967	0.88[ASN][1000 genomes]
rs4768221	0.88[ASN][1000 genomes]
rs6581514	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6581519	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7132203	0.82[EUR][1000 genomes]
rs71443907	0.83[AMR][1000 genomes]
rs716231	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs722817	0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs728622	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728623	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728624	0.94[ASN][1000 genomes]
rs729216	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7306140	0.85[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7310430	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs878010	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs900253	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs937109	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs937110	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs937111	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];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	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv899030	chr12:40509341-40580440	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv899031	chr12:40520684-40580440	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1045516	chr12:40543200-40589557	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
5	esv3398206	chr12:40556364-40581392	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1948380	SLC2A13	cis	parietal	SCAN
rs1948380	ZCRB1	cis	parietal	SCAN
rs1948380	LRRK2	cis	parietal	SCAN
rs1948380	SLC2A13	Cis_1M	lymphoblastoid	RTeQTL
rs1948380	LRRK2	cis	cerebellum	SCAN
rs1948380	AC079630.2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40557400-40564600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:40561800-40563200	Enhancers	Primary B cells from cord blood	blood
3	chr12:40562000-40563000	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr12:40562000-40563000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr12:40562000-40563200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:40562200-40563000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr12:40562400-40563000	Enhancers	Primary T cells from cord blood	blood
8	chr12:40562600-40563000	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr12:40562800-40564400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr12:40562800-40565600	Enhancers	GM12878-XiMat	blood

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