Variant report

Variant	rs4517490
Chromosome Location	chr11:17043054-17043055
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:17043020..17045707-chr11:17047002..17049137,2	MCF-7	breast:
2	chr11:17042951..17044866-chr11:17096033..17099026,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NUCB2-6	chr11:17042246-17043656	NONHSAT018198

Variant related genes	Relation type
ENSG00000272034	Chromatin interaction
ENSG00000201403	Chromatin interaction
ENSG00000110700	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10766373	0.87[ASN][1000 genomes]
rs10832725	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10832727	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10832729	0.80[ASN][1000 genomes]
rs11024113	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024116	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024130	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024131	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024149	0.87[ASN][1000 genomes]
rs11024151	0.85[ASN][1000 genomes]
rs12288579	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12293395	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12794156	0.85[EUR][1000 genomes]
rs17472886	0.89[ASN][1000 genomes]
rs34902253	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4255517	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4456241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4468326	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56030184	0.81[EUR][1000 genomes]
rs6486345	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6486346	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6486347	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6486348	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7104247	0.90[ASN][1000 genomes]
rs71047522	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7106954	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7107283	0.84[ASN][1000 genomes]
rs7117166	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7130826	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7924495	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7927240	0.86[ASN][1000 genomes]
rs7929927	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930058	0.92[ASN][1000 genomes]
rs7932916	0.83[ASN][1000 genomes]
rs7934571	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7934608	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7934694	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7935162	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7935420	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7935677	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7937880	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7938820	0.86[ASN][1000 genomes]
rs7939614	0.89[ASN][1000 genomes]
rs7939750	0.89[ASN][1000 genomes]
rs7946165	0.89[ASN][1000 genomes]
rs7949405	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7950225	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7952426	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9919540	0.89[ASN][1000 genomes]
rs9919600	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv825771	chr11:17027229-17048360	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	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
4	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
rs4517490	NUCB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 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	chr11:17037400-17044400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr11:17037600-17046400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:17037600-17048400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr11:17037600-17049400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr11:17037600-17058400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr11:17037600-17058600	Weak transcription	Gastric	stomach
10	chr11:17037800-17044600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr11:17037800-17048200	Weak transcription	Stomach Mucosa	stomach
12	chr11:17037800-17057400	Weak transcription	Fetal Stomach	stomach
13	chr11:17037800-17057800	Weak transcription	Pancreas	Pancrea
14	chr11:17038800-17046200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr11:17039600-17049600	Weak transcription	Thymus	Thymus
16	chr11:17041200-17051800	Weak transcription	Fetal Intestine Large	intestine
17	chr11:17042000-17043600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr11:17042400-17043200	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr11:17042400-17043400	Strong transcription	Liver	Liver
20	chr11:17042400-17043400	Enhancers	A549	lung
21	chr11:17042400-17048200	Weak transcription	HepG2	liver
22	chr11:17042600-17043200	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr11:17042600-17043400	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr11:17042600-17043400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr11:17042600-17043800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr11:17042600-17044400	Strong transcription	Fetal Intestine Small	intestine
27	chr11:17042800-17043200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr11:17042800-17043400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr11:17042800-17043600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr11:17042800-17043800	Enhancers	Placenta	Placenta
31	chr11:17043000-17043200	Enhancers	Muscle Satellite Cultured Cells	--
32	chr11:17043000-17043400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr11:17043000-17043400	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr11:17043000-17043400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr11:17043000-17043600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
36	chr11:17043000-17048400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr11:17043000-17048600	Weak transcription	HSMM	muscle
38	chr11:17043000-17049000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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