Variant report

Variant	rs469991
Chromosome Location	chr22:29307859-29307860
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29298276..29299796-chr22:29305846..29307998,2	MCF-7	breast:
2	chr22:29194488..29196341-chr22:29307007..29309890,3	MCF-7	breast:
3	chr22:29307320..29309018-chr22:29331038..29332633,2	K562	blood:
4	chr22:29302324..29303849-chr22:29306626..29308399,2	MCF-7	breast:
5	chr22:29280624..29284164-chr22:29307760..29311501,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100219	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1065497	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12165962	0.84[JPT][hapmap]
rs1318025	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1318026	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs132528	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs132529	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs132531	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs132533	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs132536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs132543	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs132548	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2015500	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2064261	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2097461	0.83[CEU][hapmap];0.84[JPT][hapmap]
rs2213645	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2239815	0.89[JPT][hapmap]
rs2239828	0.96[CEU][hapmap]
rs2269577	0.83[CEU][hapmap];0.84[JPT][hapmap]
rs2347447	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs3788409	0.83[CEU][hapmap];0.89[JPT][hapmap];0.80[YRI][hapmap]
rs469990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs469992	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4822998	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs5752809	0.83[CEU][hapmap];0.84[JPT][hapmap]
rs5752812	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs5752826	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5762784	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs5762788	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs5762795	0.89[JPT][hapmap]
rs5762870	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5762874	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5762877	0.94[ASN][1000 genomes]
rs5762880	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5762881	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5762882	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5762936	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs5997408	0.84[JPT][hapmap]
rs5997412	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6005881	0.89[JPT][hapmap]
rs6005915	0.95[JPT][hapmap]
rs6005936	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6519766	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs715531	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7287806	0.89[JPT][hapmap]
rs7287918	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs763073	0.89[JPT][hapmap]
rs8136297	0.82[EUR][1000 genomes]
rs8137262	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8142067	0.91[EUR][1000 genomes]
rs9620841	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9625619	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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
rs469991	XBP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 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	chr22:29299000-29309200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr22:29303800-29313200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr22:29304400-29309400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr22:29304400-29312400	Weak transcription	Fetal Brain Female	brain
8	chr22:29304400-29312600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr22:29304600-29312600	Weak transcription	Fetal Brain Male	brain
10	chr22:29304600-29313000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr22:29304800-29313800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr22:29305000-29312600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr22:29305000-29313600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr22:29305400-29309600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr22:29305600-29313600	Weak transcription	NHEK	skin
16	chr22:29305800-29310000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr22:29306200-29308000	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr22:29306200-29308400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr22:29306200-29308400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr22:29306400-29308000	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr22:29306400-29308200	Enhancers	Right Ventricle	heart
22	chr22:29306400-29308600	Enhancers	Fetal Heart	heart
23	chr22:29306400-29308600	Enhancers	Fetal Muscle Leg	muscle
24	chr22:29306400-29308600	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr22:29306400-29308600	Enhancers	Hela-S3	cervix
26	chr22:29306400-29309200	Enhancers	Liver	Liver
27	chr22:29306400-29309200	Enhancers	Placenta	Placenta
28	chr22:29306400-29309600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr22:29306400-29309800	Enhancers	Rectal Smooth Muscle	rectum
30	chr22:29306400-29310400	Enhancers	Colon Smooth Muscle	Colon
31	chr22:29306400-29310400	Enhancers	Fetal Lung	lung
32	chr22:29306400-29311200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr22:29306600-29308000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr22:29306600-29308000	Enhancers	Aorta	Aorta
35	chr22:29306600-29308200	Enhancers	Ovary	ovary
36	chr22:29306600-29308400	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr22:29306600-29308400	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr22:29306600-29308400	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr22:29306600-29308400	Enhancers	Fetal Stomach	stomach
40	chr22:29306600-29308400	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr22:29306600-29308600	Enhancers	Adipose Nuclei	Adipose
42	chr22:29306600-29308600	Enhancers	Left Ventricle	heart
43	chr22:29306600-29308600	Enhancers	Pancreas	Pancrea
44	chr22:29306600-29308600	Enhancers	Right Atrium	heart
45	chr22:29306600-29308600	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr22:29306600-29308600	Enhancers	Osteobl	bone
47	chr22:29306600-29309200	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr22:29306800-29308000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr22:29306800-29308200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr22:29306800-29308600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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