Variant report

Variant	rs4563220
Chromosome Location	chr2:152804838-152804839
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:152803348..152805157-chr2:152810668..152812299,2	K562	blood:
2	chr2:152683277..152685736-chr2:152803172..152805723,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162980	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10930837	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10930853	0.85[AMR][1000 genomes]
rs12463883	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1356732	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1474172	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs1519710	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs16830434	1.00[CEU][hapmap]
rs16830435	1.00[CEU][hapmap];0.83[GIH][hapmap]
rs16830450	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs16830539	1.00[CEU][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes]
rs3754532	1.00[CEU][hapmap]
rs4496331	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6730903	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72621650	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7562260	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7571876	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7580901	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs7581344	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs7597915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs867544	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs883157	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs883170	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs952339	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3693431	chr2:152683731-152981827	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv875290	chr2:152803129-152920126	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4563220	XBP1	trans	brain	seeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152801200-152805000	Enhancers	Placenta	Placenta
2	chr2:152801800-152805000	Enhancers	NHEK	skin
3	chr2:152802000-152809800	Weak transcription	HepG2	liver
4	chr2:152802800-152805000	Enhancers	Fetal Muscle Leg	muscle
5	chr2:152802800-152805000	Enhancers	Fetal Thymus	thymus
6	chr2:152803000-152805400	Enhancers	Brain Substantia Nigra	brain
7	chr2:152803600-152805200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:152803800-152805000	Enhancers	Fetal Lung	lung
9	chr2:152804000-152805000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:152804000-152805400	Enhancers	Esophagus	oesophagus
11	chr2:152804400-152805000	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr2:152804400-152805400	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr2:152804400-152805600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:152804400-152805800	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr2:152804400-152806000	Enhancers	Brain Hippocampus Middle	brain
16	chr2:152804400-152809600	Weak transcription	Psoas Muscle	Psoas
17	chr2:152804600-152805000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:152804600-152805000	Enhancers	Brain Anterior Caudate	brain
19	chr2:152804600-152805000	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr2:152804600-152805000	Enhancers	Stomach Smooth Muscle	stomach
21	chr2:152804600-152805400	Enhancers	Aorta	Aorta
22	chr2:152804600-152805400	Enhancers	Brain Angular Gyrus	brain
23	chr2:152804600-152805600	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr2:152804600-152805800	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr2:152804600-152806200	Enhancers	Adipose Nuclei	Adipose
26	chr2:152804600-152807000	Weak transcription	Lung	lung
27	chr2:152804600-152808000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:152804600-152828400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:152804800-152805000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:152804800-152805000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:152804800-152805000	Enhancers	Fetal Brain Female	brain
32	chr2:152804800-152805200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:152804800-152805400	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr2:152804800-152805400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:152804800-152808000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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