Variant report

Variant	rs11752777
Chromosome Location	chr6:5695126-5695127
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NRN1-7	chr6:5695115-5695241	ENSG00000270174.1

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1001568	0.94[CHB][hapmap]
rs13213128	0.85[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2005970	0.89[ASN][1000 genomes]
rs2142738	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2326634	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4140654	0.81[CEU][hapmap];0.80[JPT][hapmap]
rs4959347	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4960125	0.85[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4960126	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62385480	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62408067	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6918561	0.90[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap]
rs6918675	0.85[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap]
rs6935719	0.81[ASN][1000 genomes]
rs760675	0.81[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs7739358	0.81[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap]
rs7746913	0.80[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs877010	0.82[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs878988	0.85[CEU][hapmap];0.80[JPT][hapmap]
rs9328328	0.94[CHB][hapmap]
rs9378979	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9378980	0.85[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9378983	0.90[CHB][hapmap]
rs9392709	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9392710	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9405280	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9405281	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.80[TSI][hapmap];0.85[ASN][1000 genomes]
rs9405859	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9405861	0.84[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs9502329	0.80[ASN][1000 genomes]
rs9504488	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv3473790	chr6:5692573-5707035	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv3473791	chr6:5692573-5707035	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv823407	chr6:5692735-5706712	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv970201	chr6:5693538-5699453	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv3360474	chr6:5694654-5695163	Weak transcription Enhancers Strong transcription Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11752777	NQO2	cis	parietal	SCAN
rs11752777	C6orf201	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5672200-5705800	Weak transcription	Thymus	Thymus
2	chr6:5673800-5701200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr6:5673800-5709800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:5678000-5709400	Weak transcription	Pancreas	Pancrea
5	chr6:5680600-5695400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:5682400-5695200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr6:5682400-5695400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:5684600-5695400	Weak transcription	Fetal Stomach	stomach
9	chr6:5684800-5696000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:5684800-5706000	Weak transcription	Ovary	ovary
11	chr6:5685000-5695400	Weak transcription	HSMMtube	muscle
12	chr6:5685000-5698600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:5691400-5698200	Weak transcription	Spleen	Spleen
14	chr6:5692800-5701400	Weak transcription	Right Atrium	heart
15	chr6:5693000-5696000	Weak transcription	Fetal Intestine Small	intestine
16	chr6:5693400-5695200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:5694200-5695400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:5694200-5695800	Weak transcription	NH-A	brain
19	chr6:5694800-5696400	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr6:5694800-5696400	Enhancers	Fetal Thymus	thymus
21	chr6:5695000-5695200	Enhancers	Primary T cells from cord blood	blood
22	chr6:5695000-5695200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:5695000-5695200	Enhancers	NHDF-Ad	bronchial
24	chr6:5695000-5695400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:5695000-5695800	Enhancers	Primary T cells fromperipheralblood	blood
26	chr6:5695000-5696200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr6:5695000-5696400	Enhancers	Dnd41	blood
28	chr6:5695000-5696600	Enhancers	Primary monocytes fromperipheralblood	blood

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