Variant report

Variant	rs214083
Chromosome Location	chr11:17298859-17298860
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:17097827..17101102-chr11:17296839..17299555,4	K562	blood:
2	chr11:17229045..17230754-chr11:17298034..17300385,2	MCF-7	breast:
3	chr11:17297082..17301177-chr11:17313853..17317788,6	K562	blood:
4	chr11:17097070..17101102-chr11:17296326..17299484,3	K562	blood:
5	chr11:17289393..17293255-chr11:17296129..17299283,5	K562	blood:
6	chr11:17294885..17299963-chr11:17371989..17377835,11	K562	blood:
7	chr11:17229425..17232064-chr11:17297458..17300131,2	K562	blood:
8	chr11:17296907..17298912-chr11:17352213..17353767,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000188211	Chromatin interaction
ENSG00000201403	Chromatin interaction
ENSG00000011405	Chromatin interaction
ENSG00000110700	Chromatin interaction
ENSG00000070081	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs105290	0.86[ASN][1000 genomes]
rs10741724	0.81[ASN][1000 genomes]
rs10741725	0.96[YRI][hapmap]
rs10766381	0.88[ASN][1000 genomes]
rs10766382	0.84[ASN][1000 genomes]
rs10832733	0.92[JPT][hapmap]
rs10832745	0.86[ASN][1000 genomes]
rs10832746	0.86[ASN][1000 genomes]
rs10832747	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs10832748	0.82[ASN][1000 genomes]
rs10832750	0.82[ASN][1000 genomes]
rs10832752	0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs11024158	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs11024204	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs11024207	0.88[ASN][1000 genomes]
rs11024208	0.88[ASN][1000 genomes]
rs11024220	0.84[ASN][1000 genomes]
rs11024221	0.84[ASN][1000 genomes]
rs11024223	0.92[CHB][hapmap];0.84[ASN][1000 genomes]
rs11024229	0.86[ASN][1000 genomes]
rs11024231	0.86[ASN][1000 genomes]
rs1125737	0.83[ASN][1000 genomes]
rs12276859	0.84[ASN][1000 genomes]
rs12280930	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs12286505	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs1488933	0.84[ASN][1000 genomes]
rs190046	0.86[ASN][1000 genomes]
rs1979603	0.93[ASN][1000 genomes]
rs214068	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs214069	0.82[ASN][1000 genomes]
rs214071	0.92[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs214075	0.92[CHB][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.88[ASN][1000 genomes]
rs214076	0.84[CHB][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.88[ASN][1000 genomes]
rs214077	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs214079	0.88[ASN][1000 genomes]
rs214080	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs214081	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs214082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs214084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs214085	0.88[ASN][1000 genomes]
rs214087	0.90[ASN][1000 genomes]
rs214088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs214092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs214093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs214094	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs214095	0.84[ASN][1000 genomes]
rs214097	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs214099	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs214101	0.92[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.80[ASN][1000 genomes]
rs214102	0.86[ASN][1000 genomes]
rs214106	0.96[YRI][hapmap]
rs214900	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs214901	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs214909	0.84[ASN][1000 genomes]
rs214910	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs214913	0.82[ASN][1000 genomes]
rs214914	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs214915	0.84[ASN][1000 genomes]
rs214916	0.84[ASN][1000 genomes]
rs214918	0.84[ASN][1000 genomes]
rs214919	0.84[ASN][1000 genomes]
rs214920	0.84[ASN][1000 genomes]
rs214921	0.84[ASN][1000 genomes]
rs214922	0.84[ASN][1000 genomes]
rs214925	1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs214935	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs214936	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs214939	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs214940	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs2171615	0.82[ASN][1000 genomes]
rs4356203	0.92[JPT][hapmap]
rs4508187	0.84[ASN][1000 genomes]
rs4509731	0.85[ASN][1000 genomes]
rs512852	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs603618	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs61357262	0.83[ASN][1000 genomes]
rs615358	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs618331	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs677540	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs7101686	0.82[ASN][1000 genomes]
rs7108315	0.84[ASN][1000 genomes]
rs7108316	0.80[ASN][1000 genomes]
rs7118443	0.81[ASN][1000 genomes]
rs7123301	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs7128822	0.84[ASN][1000 genomes]
rs7342262	1.00[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs7925692	1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs7937176	0.90[ASN][1000 genomes]
rs7940253	0.80[ASN][1000 genomes]
rs7949699	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv469762	chr11:17170690-17320691	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv482905	chr11:17170690-17320691	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	esv1836937	chr11:17291499-17339127	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs214083	NUCB2	cis	Lymphoblastoid	GTEx
rs214083	OR7E14P	cis	Esophagus Mucosa	GTEx
rs214083	OR7E14P	cis	Nerve Tibial	GTEx
rs214083	NUCB2	Cis_1M	lymphoblastoid	RTeQTL
rs214083	NUCB2	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17297000-17299200	Active TSS	Fetal Kidney	kidney
2	chr11:17297000-17299200	Active TSS	Rectal Smooth Muscle	rectum
3	chr11:17297400-17299200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr11:17297400-17299400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr11:17297400-17299400	Active TSS	Brain Angular Gyrus	brain
6	chr11:17297600-17299000	Active TSS	H9 Cell Line	embryonic stem cell
7	chr11:17297600-17299000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:17297600-17299000	Active TSS	Aorta	Aorta
9	chr11:17297600-17299000	Active TSS	Fetal Brain Female	brain
10	chr11:17297600-17299000	Active TSS	Left Ventricle	heart
11	chr11:17297600-17299000	Active TSS	Ovary	ovary
12	chr11:17297600-17299000	Active TSS	Pancreas	Pancrea
13	chr11:17297600-17299000	Active TSS	HSMM	muscle
14	chr11:17297600-17299200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:17297600-17299200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:17297600-17299200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr11:17297600-17299200	Active TSS	Colonic Mucosa	Colon
18	chr11:17297600-17299200	Active TSS	Colon Smooth Muscle	Colon
19	chr11:17297600-17299200	Active TSS	Fetal Stomach	stomach
20	chr11:17297600-17299200	Active TSS	Psoas Muscle	Psoas
21	chr11:17297600-17299200	Active TSS	Right Atrium	heart
22	chr11:17297600-17299200	Active TSS	Right Ventricle	heart
23	chr11:17297600-17299400	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr11:17297600-17299400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr11:17297600-17299400	Active TSS	Brain Germinal Matrix	brain
26	chr11:17297600-17299400	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr11:17297800-17299000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr11:17297800-17299000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:17297800-17299000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr11:17297800-17299000	Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr11:17297800-17299000	Active TSS	Brain Hippocampus Middle	brain
32	chr11:17297800-17299000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr11:17297800-17299000	Active TSS	Esophagus	oesophagus
34	chr11:17297800-17299000	Active TSS	Gastric	stomach
35	chr11:17297800-17299000	Active TSS	Lung	lung
36	chr11:17297800-17299000	Active TSS	Sigmoid Colon	Sigmoid Colon
37	chr11:17297800-17299000	Active TSS	Small Intestine	intestine
38	chr11:17297800-17299000	Active TSS	Spleen	Spleen
39	chr11:17297800-17299000	Active TSS	A549	lung
40	chr11:17297800-17299000	Bivalent/Poised TSS	HepG2	liver
41	chr11:17297800-17299200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr11:17297800-17299200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr11:17297800-17299200	Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr11:17297800-17299200	Active TSS	Brain Substantia Nigra	brain
45	chr11:17297800-17299200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr11:17297800-17299200	Active TSS	Stomach Mucosa	stomach
47	chr11:17297800-17299400	Active TSS	Brain Anterior Caudate	brain
48	chr11:17297800-17299400	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr11:17297800-17299400	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr11:17297800-17299400	Active TSS	Rectal Mucosa Donor 29	rectum

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