Variant report

Variant	rs11024621
Chromosome Location	chr11:18340241-18340242
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:18339772..18342486-chr11:18375558..18377297,2	K562	blood:
2	chr11:18338559..18340815-chr11:18429973..18431538,2	K562	blood:
3	chr11:18338584..18340305-chr11:18416073..18417820,2	K562	blood:
4	chr11:18339570..18341563-chr11:18389035..18391001,2	K562	blood:
5	chr11:18339644..18341634-chr11:18415922..18417632,2	MCF-7	breast:
6	chr11:18307340..18310591-chr11:18340181..18344104,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110756	Chromatin interaction
ENSG00000134333	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10832918	0.83[JPT][hapmap]
rs11024605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024607	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024611	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[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];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024619	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11024625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024632	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12221676	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12224608	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];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1869786	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869787	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305565	0.80[ASN][1000 genomes]
rs3781944	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]
rs4150530	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4150572	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4150626	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4150635	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4150658	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4237721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4344464	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4366463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4586132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756938	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757638	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs4757639	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757642	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4757646	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs60677587	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7113249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7122032	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]
rs7128017	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128146	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73430865	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73430866	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73430881	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73430888	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73430894	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73432712	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73434649	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9783296	0.84[AMR][1000 genomes];0.89[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11024621	NUCB2	cis	cerebellum	SCAN
rs11024621	HPS5	cis	multi-tissue	Pritchard

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18311800-18343000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:18317200-18342200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:18327800-18342200	Weak transcription	Colon Smooth Muscle	Colon
4	chr11:18327800-18342200	Weak transcription	HUVEC	blood vessel
5	chr11:18330200-18340800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr11:18331000-18341000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr11:18331000-18341600	Weak transcription	Fetal Lung	lung
8	chr11:18331000-18342200	Weak transcription	Right Ventricle	heart
9	chr11:18331600-18341600	Weak transcription	Psoas Muscle	Psoas
10	chr11:18332000-18341800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:18332200-18342200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr11:18332600-18341000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr11:18332600-18342800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr11:18332600-18342800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr11:18332600-18343000	Weak transcription	Lung	lung
16	chr11:18332800-18340800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr11:18332800-18341000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr11:18332800-18341800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr11:18332800-18341800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr11:18332800-18342200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr11:18332800-18342200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr11:18332800-18342800	Weak transcription	Fetal Brain Male	brain
23	chr11:18333000-18341600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr11:18333000-18341800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr11:18333000-18341800	Weak transcription	Thymus	Thymus
26	chr11:18333000-18342000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr11:18333000-18342000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr11:18333000-18342000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr11:18333000-18342200	Weak transcription	Adipose Nuclei	Adipose
30	chr11:18333000-18342400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr11:18333000-18342400	Weak transcription	Colonic Mucosa	Colon
32	chr11:18333000-18342800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr11:18333000-18342800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr11:18333200-18342200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr11:18333600-18341000	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr11:18333800-18340800	Weak transcription	Brain Germinal Matrix	brain
37	chr11:18334000-18341800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr11:18334400-18341200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr11:18334400-18341200	Weak transcription	Brain Hippocampus Middle	brain
40	chr11:18334400-18341600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr11:18334400-18341600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr11:18334400-18342800	Weak transcription	Fetal Thymus	thymus
43	chr11:18334400-18343000	Weak transcription	Esophagus	oesophagus
44	chr11:18334400-18343200	Weak transcription	Pancreas	Pancrea
45	chr11:18334600-18341400	Weak transcription	Fetal Intestine Large	intestine
46	chr11:18334600-18342200	Weak transcription	Brain Angular Gyrus	brain
47	chr11:18334600-18342200	Weak transcription	Brain Anterior Caudate	brain
48	chr11:18334600-18342200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr11:18334600-18342200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr11:18334800-18341400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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