Variant report

Variant	rs11068945
Chromosome Location	chr12:118867664-118867665
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SUDS3-1	chr12:118867635-118867734	l_738_chr12:118861629-118875945_testes

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10850968	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10850969	0.98[ASN][1000 genomes]
rs10850970	1.00[ASN][1000 genomes]
rs11068864	1.00[EUR][1000 genomes]
rs11068865	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068871	1.00[EUR][1000 genomes]
rs11068872	0.83[EUR][1000 genomes]
rs11068878	1.00[EUR][1000 genomes]
rs11068880	0.89[CHB][hapmap];1.00[EUR][1000 genomes]
rs11068881	1.00[EUR][1000 genomes]
rs11068883	0.85[AMR][1000 genomes]
rs11068887	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068888	1.00[EUR][1000 genomes]
rs11068889	1.00[EUR][1000 genomes]
rs11068891	0.83[CHB][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap]
rs11068893	0.89[CHB][hapmap];1.00[EUR][1000 genomes]
rs11068896	1.00[EUR][1000 genomes]
rs11068898	0.89[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[EUR][1000 genomes]
rs11068899	1.00[EUR][1000 genomes]
rs11068900	0.88[CHB][hapmap]
rs11068901	1.00[ASW][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11068904	0.94[CHB][hapmap];1.00[EUR][1000 genomes]
rs11068908	0.83[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap]
rs11068909	1.00[ASW][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11068914	0.83[EUR][1000 genomes]
rs11068915	0.89[CHB][hapmap];1.00[EUR][1000 genomes]
rs11068916	0.88[CHB][hapmap];0.81[JPT][hapmap];1.00[EUR][1000 genomes]
rs11068917	0.83[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap]
rs11068919	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs11068920	1.00[EUR][1000 genomes]
rs11068923	1.00[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11068924	1.00[EUR][1000 genomes]
rs11068930	1.00[EUR][1000 genomes]
rs11068933	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11068937	1.00[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11068940	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068941	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068943	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12227411	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12227974	0.89[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12228425	0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12230104	1.00[EUR][1000 genomes]
rs12231358	1.00[EUR][1000 genomes]
rs12231845	1.00[EUR][1000 genomes]
rs16948250	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs17586582	0.89[CHB][hapmap];1.00[EUR][1000 genomes]
rs17619702	0.86[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17619805	0.89[CHB][hapmap];1.00[EUR][1000 genomes]
rs17619932	0.83[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs2062520	1.00[EUR][1000 genomes]
rs2271007	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3741444	1.00[EUR][1000 genomes]
rs56080343	0.97[ASN][1000 genomes]
rs7132582	1.00[EUR][1000 genomes]
rs7296216	1.00[EUR][1000 genomes]
rs7974718	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs9888447	0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][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	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv899547	chr12:118791441-118896304	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv930978	chr12:118866332-119450600	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11068945	SUDS3	cis	lymphoblastoid	seeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118854000-118870800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:118854600-118870800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:118854600-118874400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr12:118854800-118870600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:118854800-118874400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr12:118855200-118868200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr12:118855200-118870000	Weak transcription	Brain Hippocampus Middle	brain
8	chr12:118855200-118874200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:118856600-118868200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr12:118856800-118868400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:118857000-118874400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:118857400-118869000	Weak transcription	Primary T cells from cord blood	blood
13	chr12:118857400-118870600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr12:118866600-118867800	Enhancers	Adipose Nuclei	Adipose
15	chr12:118867600-118867800	Enhancers	Ovary	ovary
16	chr12:118867600-118867800	Enhancers	Pancreas	Pancrea
17	chr12:118867600-118867800	Enhancers	Psoas Muscle	Psoas
18	chr12:118867600-118867800	Enhancers	Small Intestine	intestine
19	chr12:118867600-118868000	Enhancers	Gastric	stomach
20	chr12:118867600-118868000	Enhancers	Lung	lung
21	chr12:118867600-118868000	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr12:118867600-118868600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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