Variant report

Variant	rs3781944
Chromosome Location	chr11:18328426-18328427
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18328369..18330442-chr11:18341510..18343181,2	K562	blood:
2	chr11:18326938..18329075-chr11:18343306..18345180,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110768	Chromatin interaction
ENSG00000110756	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10832918	0.83[JPT][hapmap]
rs11024605	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024607	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024614	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs11024615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024619	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11024621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024625	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024632	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12221676	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12224608	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1869786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305565	0.80[ASN][1000 genomes]
rs4150530	0.92[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];0.82[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4150572	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4150626	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4150635	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4150656	0.83[AFR][1000 genomes]
rs4150658	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4237721	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4344464	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4366463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4586132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756938	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757638	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs4757639	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757642	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4757645	0.89[YRI][hapmap]
rs4757646	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60677587	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7113249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7122032	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128017	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128146	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73430865	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73430866	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73430881	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73430888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73430894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73432712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73434649	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9783296	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv428569	chr11:18194030-18350869	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv933836	chr11:18300254-18440933	Active TSS Weak transcription Strong transcription Enhancers Flanking 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 miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3781944	NUCB2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18287600-18334000	Weak transcription	Right Atrium	heart
2	chr11:18298200-18333800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:18298800-18331600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr11:18299200-18332400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr11:18299600-18334200	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr11:18300000-18328600	Weak transcription	Stomach Mucosa	stomach
7	chr11:18300000-18334400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr11:18300200-18333600	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr11:18300200-18334000	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr11:18300200-18334800	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr11:18300200-18336000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr11:18300600-18331600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr11:18300600-18332600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr11:18300600-18333200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr11:18300600-18334000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr11:18300800-18330200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr11:18300800-18333000	Strong transcription	Dnd41	blood
18	chr11:18301000-18334400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr11:18302200-18333000	Strong transcription	Adipose Nuclei	Adipose
20	chr11:18303000-18334800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr11:18303200-18334800	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr11:18303400-18335000	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr11:18304400-18332000	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr11:18304600-18332000	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr11:18305000-18331600	Strong transcription	Primary B cells from peripheral blood	blood
26	chr11:18305200-18332000	Strong transcription	Primary B cells from cord blood	blood
27	chr11:18305600-18335000	Strong transcription	Primary T cells from cord blood	blood
28	chr11:18307400-18332400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr11:18308000-18333000	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr11:18309000-18331600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr11:18310800-18334000	Weak transcription	Esophagus	oesophagus
32	chr11:18311800-18343000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:18312800-18334400	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr11:18313000-18333000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr11:18314800-18330000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr11:18315200-18332000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr11:18316200-18333800	Weak transcription	Fetal Heart	heart
38	chr11:18316800-18332200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr11:18317000-18330000	Weak transcription	Fetal Brain Male	brain
40	chr11:18317200-18330600	Weak transcription	Lung	lung
41	chr11:18317200-18342200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr11:18318200-18329600	Weak transcription	Colonic Mucosa	Colon
43	chr11:18318800-18329800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr11:18319000-18331600	Weak transcription	Small Intestine	intestine
45	chr11:18319000-18334000	Weak transcription	NHLF	lung
46	chr11:18319200-18331400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr11:18319200-18331600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr11:18319400-18330200	Weak transcription	Psoas Muscle	Psoas
49	chr11:18320000-18332800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr11:18320400-18329600	Weak transcription	Pancreas	Pancrea

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