Variant report

Variant	rs469989
Chromosome Location	chr22:29303595-29303596
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29302324..29303849-chr22:29306626..29308399,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12165962	0.81[CEU][hapmap]
rs132534	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs132539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2097461	0.87[CEU][hapmap]
rs2239815	0.82[CEU][hapmap]
rs2269577	0.87[CEU][hapmap]
rs2347447	0.86[CEU][hapmap]
rs3788409	0.86[CEU][hapmap]
rs5752797	0.82[JPT][hapmap]
rs5752809	0.86[CEU][hapmap]
rs5752812	0.86[CEU][hapmap]
rs5762784	0.86[CEU][hapmap]
rs5762788	0.86[CEU][hapmap]
rs5762795	0.82[CEU][hapmap]
rs5762877	0.90[EUR][1000 genomes]
rs5997408	0.83[CEU][hapmap]
rs7287806	0.82[CEU][hapmap]
rs763073	0.82[CEU][hapmap]
rs8141529	0.90[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs469989	XBP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29296800-29310200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr22:29298400-29308400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr22:29298400-29310400	Enhancers	Fetal Intestine Large	intestine
4	chr22:29298600-29304600	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr22:29298600-29305000	Enhancers	Brain Anterior Caudate	brain
6	chr22:29298600-29305400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr22:29298800-29304400	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr22:29298800-29305200	Enhancers	Brain Cingulate Gyrus	brain
9	chr22:29299000-29309200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr22:29299200-29304400	Weak transcription	Brain Germinal Matrix	brain
11	chr22:29299600-29307000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr22:29299800-29303800	Enhancers	Pancreas	Pancrea
13	chr22:29300000-29303600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr22:29300000-29307600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr22:29300200-29303600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr22:29300200-29303600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr22:29300600-29304000	Weak transcription	A549	lung
18	chr22:29300800-29303600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr22:29300800-29303600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr22:29300800-29304400	Enhancers	Stomach Smooth Muscle	stomach
21	chr22:29300800-29307000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr22:29300800-29307400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr22:29300800-29307600	Weak transcription	Small Intestine	intestine
24	chr22:29301000-29303600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr22:29301000-29304200	Weak transcription	NHEK	skin
26	chr22:29301000-29304600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr22:29301000-29304600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr22:29301000-29304800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr22:29301000-29305400	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr22:29301000-29305400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr22:29301000-29306800	Weak transcription	NHLF	lung
32	chr22:29301200-29303600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr22:29301200-29304200	Weak transcription	Fetal Muscle Leg	muscle
34	chr22:29301200-29306400	Weak transcription	Fetal Heart	heart
35	chr22:29301200-29306600	Weak transcription	Adipose Nuclei	Adipose
36	chr22:29301400-29303600	Weak transcription	Right Ventricle	heart
37	chr22:29301400-29306600	Weak transcription	Fetal Stomach	stomach
38	chr22:29301400-29306800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr22:29301400-29306800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr22:29301600-29304400	Enhancers	Brain Hippocampus Middle	brain
41	chr22:29301800-29304600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr22:29301800-29304800	Weak transcription	Esophagus	oesophagus
43	chr22:29301800-29306600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr22:29301800-29307200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr22:29302000-29303800	Enhancers	Aorta	Aorta
46	chr22:29302000-29307400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr22:29302200-29304000	Enhancers	Left Ventricle	heart
48	chr22:29302400-29304400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr22:29302400-29304600	Genic enhancers	HepG2	liver
50	chr22:29302400-29304800	Enhancers	Brain Angular Gyrus	brain

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