Variant report

Variant	rs7933966
Chromosome Location	chr11:32875597-32875598
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC73-1	chr11:32875249-32875810	ENSG00000248689
2	lnc-QSER1-1	chr11:32875249-32875808	NONHSAT018678

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10488703	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.94[ASN][1000 genomes]
rs10488704	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10767970	0.87[CHB][hapmap]
rs10767971	0.97[ASN][1000 genomes]
rs10767972	0.97[ASN][1000 genomes]
rs10835981	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs10835983	0.98[ASN][1000 genomes]
rs10835989	0.87[ASN][1000 genomes]
rs11032024	0.98[ASN][1000 genomes]
rs11032025	0.87[CHB][hapmap];0.80[CHD][hapmap]
rs11032032	0.98[ASN][1000 genomes]
rs11032033	0.98[ASN][1000 genomes]
rs11032034	0.98[ASN][1000 genomes]
rs11032044	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs11032046	0.95[ASN][1000 genomes]
rs11032047	0.95[ASN][1000 genomes]
rs11821224	0.90[ASN][1000 genomes]
rs11826294	0.94[ASN][1000 genomes]
rs16923617	0.92[ASN][1000 genomes]
rs197705	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs197707	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs197710	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2664692	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28449959	0.92[ASN][1000 genomes]
rs2900981	0.88[ASN][1000 genomes]
rs4755454	0.89[ASN][1000 genomes]
rs4756329	0.87[CHB][hapmap]
rs55744018	0.92[ASN][1000 genomes]
rs55763432	0.97[ASN][1000 genomes]
rs56230223	0.92[ASN][1000 genomes]
rs60475066	0.92[ASN][1000 genomes]
rs60529855	0.86[ASN][1000 genomes]
rs7118630	0.95[ASN][1000 genomes]
rs7122029	0.85[ASN][1000 genomes]
rs7122130	0.85[ASN][1000 genomes]
rs72899241	0.91[ASN][1000 genomes]
rs72899242	0.97[ASN][1000 genomes]
rs72901219	0.95[ASN][1000 genomes]
rs72901225	0.92[ASN][1000 genomes]
rs72901227	0.92[ASN][1000 genomes]
rs7943715	0.87[ASN][1000 genomes]
rs7944652	0.87[CHB][hapmap]
rs956322	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9943603	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9943661	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758262	chr11:32714643-33049940	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	esv2759815	chr11:32714643-33049940	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	esv2757434	chr11:32792784-32958609	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv34742	chr11:32796092-33004024	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	esv2753057	chr11:32796124-33061724	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	esv2753743	chr11:32796124-33084924	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
7	nsv897190	chr11:32801921-32951836	Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv897191	chr11:32805169-32903263	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv897192	chr11:32828760-32903263	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv897193	chr11:32838288-32903263	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7933966	QSER1	cis	parietal	SCAN
rs7933966	QSER1	cis	cerebellum	SCAN
rs7933966	NAT10	cis	parietal	SCAN
rs7933966	KCNA4	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:32852200-32876800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr11:32852800-32878800	Weak transcription	Placenta	Placenta
3	chr11:32853000-32877200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:32855000-32876800	Weak transcription	Esophagus	oesophagus
5	chr11:32866000-32878200	Weak transcription	HMEC	breast
6	chr11:32869000-32878000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:32869200-32875800	Weak transcription	Spleen	Spleen
8	chr11:32872000-32882000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr11:32872200-32882200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr11:32873400-32881800	Weak transcription	Lung	lung
11	chr11:32874000-32877000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:32874000-32880600	Weak transcription	Pancreas	Pancrea
13	chr11:32874200-32877000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr11:32874200-32877400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr11:32874200-32881600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr11:32874200-32881800	Weak transcription	Fetal Intestine Large	intestine
17	chr11:32874400-32877000	Weak transcription	Hela-S3	cervix
18	chr11:32874400-32879400	Weak transcription	NHEK	skin
19	chr11:32874800-32875600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr11:32874800-32875600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:32874800-32875800	Strong transcription	Liver	Liver
22	chr11:32874800-32876000	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr11:32874800-32876000	Strong transcription	Fetal Intestine Small	intestine
24	chr11:32874800-32877400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr11:32874800-32878000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr11:32875000-32880600	Strong transcription	Monocytes-CD14+_RO01746	blood

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