Variant report

Variant	rs6486346
Chromosome Location	chr11:17049890-17049891
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NUCB2-6	chr11:17049707-17050044	NONHSAT018198

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10766373	0.86[ASN][1000 genomes]
rs10832725	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10832727	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10832729	0.81[ASN][1000 genomes]
rs10832731	0.80[ASN][1000 genomes]
rs10832733	0.81[CHB][hapmap]
rs11024113	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11024116	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11024130	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11024131	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11024148	0.90[CHB][hapmap]
rs11024149	0.88[ASN][1000 genomes]
rs11024151	0.86[ASN][1000 genomes]
rs12288579	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12293395	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12794156	0.88[EUR][1000 genomes]
rs17472886	0.88[ASN][1000 genomes]
rs214933	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs34902253	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4255517	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4456241	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4468326	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4517490	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56030184	0.84[EUR][1000 genomes]
rs6486345	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6486347	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6486348	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7104247	0.91[ASN][1000 genomes]
rs71047522	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7106954	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7107283	0.83[ASN][1000 genomes]
rs7117166	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7123825	0.84[YRI][hapmap]
rs7125607	0.91[CHB][hapmap]
rs7130826	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7924495	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7927240	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs7929927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7930058	0.93[ASN][1000 genomes]
rs7932916	0.82[ASN][1000 genomes]
rs7934571	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7934608	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7934694	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7935162	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7935420	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7935677	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7937702	0.81[AMR][1000 genomes]
rs7937880	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7938820	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs7939614	0.88[ASN][1000 genomes]
rs7939750	0.88[ASN][1000 genomes]
rs7946165	0.88[ASN][1000 genomes]
rs7949405	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949699	0.82[CHB][hapmap]
rs7950225	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7952426	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9919540	0.88[ASN][1000 genomes]
rs9919600	0.82[ASN][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	nsv832077	chr11:16834545-17059176	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv467711	chr11:17027555-17320797	Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv553568	chr11:17027555-17320797	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6486346	NUCB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17037000-17050200	Weak transcription	Adipose Nuclei	Adipose
2	chr11:17037200-17050400	Weak transcription	Brain Anterior Caudate	brain
3	chr11:17037200-17056000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr11:17037600-17058400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr11:17037600-17058600	Weak transcription	Gastric	stomach
6	chr11:17037800-17057400	Weak transcription	Fetal Stomach	stomach
7	chr11:17037800-17057800	Weak transcription	Pancreas	Pancrea
8	chr11:17041200-17051800	Weak transcription	Fetal Intestine Large	intestine
9	chr11:17045200-17050000	Strong transcription	Fetal Intestine Small	intestine
10	chr11:17046000-17056000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr11:17046800-17057400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr11:17048600-17062000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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