Variant report

Variant	rs7938541
Chromosome Location	chr11:5843785-5843786
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:5830455..5833171-chr11:5843435..5846091,2	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10047437	0.85[GIH][hapmap];0.87[EUR][1000 genomes]
rs10734554	0.87[CEU][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs10742787	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs10742788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs10742789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs10742793	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10742796	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10769224	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs10769232	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs10769235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10769236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10769240	0.87[EUR][1000 genomes]
rs10769241	0.98[ASN][1000 genomes]
rs10769247	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10838637	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10838648	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs10838653	0.87[EUR][1000 genomes]
rs10838655	0.84[ASN][1000 genomes]
rs10838666	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11039054	0.87[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap]
rs11039096	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039102	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039140	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039187	0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs11039188	0.89[ASN][1000 genomes]
rs11039193	0.90[ASN][1000 genomes]
rs11500474	0.88[EUR][1000 genomes]
rs11607346	1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12419943	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1377512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1453415	1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1453417	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1453418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1453419	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1453421	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1453424	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs1453426	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1840175	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2123663	1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2198446	0.87[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap]
rs2343154	0.98[ASN][1000 genomes]
rs4758099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4758100	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4758101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4758102	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4758103	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4758113	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap]
rs4758427	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4910844	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs4910849	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4910850	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4910851	0.90[CHB][hapmap];0.84[CHD][hapmap];0.88[ASN][1000 genomes]
rs6578689	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7484069	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs7924824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7925671	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7931236	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7935300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap]
rs7937133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7940624	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7940926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7948009	0.83[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs7949986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9651658	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046068	chr11:5335943-6063742	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv553241	chr11:5506034-6203685	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv1053414	chr11:5612989-6030212	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv530216	chr11:5614439-6468232	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv553273	chr11:5639873-5871831	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1036389	chr11:5695451-6177680	Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv540943	chr11:5695451-6177680	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
8	nsv553277	chr11:5722948-6010075	Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	esv1843296	chr11:5730377-5970717	Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
10	esv2758255	chr11:5730377-5970717	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	esv2759801	chr11:5730377-6007613	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	nsv832058	chr11:5747594-5926814	Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
13	nsv896952	chr11:5832191-5893376	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
14	nsv971927	chr11:5842082-5988665	Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv8785	chr11:5842739-5844366	Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7938541	TRIM22	cis	parietal	SCAN
rs7938541	OR52N3P	cis	Nerve Tibial	GTEx
rs7938541	OR51B5	cis	parietal	SCAN
rs7938541	OR51I1	cis	parietal	SCAN
rs7938541	RBMXL2	cis	cerebellum	SCAN
rs7938541	OR52I2	cis	cerebellum	SCAN
rs7938541	OR10A5	cis	cerebellum	SCAN
rs7938541	ASCL2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5837600-5844600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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