Variant report

Variant	rs35259224
Chromosome Location	chr22:29216603-29216604
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29215019..29217111-chr22:29277896..29279810,2	MCF-7	breast:
2	chr12:64969026..64970546-chr22:29215553..29217156,2	MCF-7	breast:
3	chr22:29167538..29169220-chr22:29214711..29217265,3	MCF-7	breast:
4	chr22:29167147..29172880-chr22:29212986..29217151,7	MCF-7	breast:
5	chr17:56735334..56737625-chr22:29214146..29217564,3	MCF-7	breast:
6	chr22:29164518..29166292-chr22:29215765..29218524,2	MCF-7	breast:
7	chr22:29126583..29142031-chr22:29203252..29220632,67	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159873	Chromatin interaction
ENSG00000100209	Chromatin interaction
ENSG00000223294	Chromatin interaction
ENSG00000183765	Chromatin interaction
ENSG00000183579	Chromatin interaction
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12628211	0.98[ASN][1000 genomes]
rs2097461	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2239815	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2269577	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2347447	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2881635	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3788409	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752795	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752798	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752801	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5752804	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752807	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752809	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752812	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752813	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762784	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5762788	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762795	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762803	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs5762815	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5762824	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762825	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762853	0.87[ASN][1000 genomes]
rs5762854	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5762859	0.82[ASN][1000 genomes]
rs5762863	0.87[ASN][1000 genomes]
rs5762864	0.87[ASN][1000 genomes]
rs5762865	0.81[EUR][1000 genomes]
rs5762867	0.81[ASN][1000 genomes]
rs5997408	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005867	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6005869	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6005872	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6005881	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6005892	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6005916	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005927	0.84[ASN][1000 genomes]
rs6005929	0.86[ASN][1000 genomes]
rs7287124	0.98[ASN][1000 genomes]
rs7287806	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs763073	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8137969	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625566	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9625588	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35259224	XBP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29197200-29231600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr22:29197400-29220400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr22:29198000-29225200	Weak transcription	HSMM	muscle
4	chr22:29198200-29218600	Weak transcription	Brain Angular Gyrus	brain
5	chr22:29198400-29225200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr22:29198600-29219400	Weak transcription	NHLF	lung
7	chr22:29198600-29225200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr22:29198600-29225200	Weak transcription	Osteobl	bone
9	chr22:29198600-29231400	Weak transcription	HSMMtube	muscle
10	chr22:29198800-29230800	Weak transcription	NHEK	skin
11	chr22:29200600-29231400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr22:29205200-29218800	Weak transcription	Brain Hippocampus Middle	brain
13	chr22:29205400-29217000	Weak transcription	Gastric	stomach
14	chr22:29205400-29225600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr22:29208200-29221000	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr22:29208400-29217000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr22:29211600-29218800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr22:29211800-29219200	Enhancers	Fetal Thymus	thymus
19	chr22:29211800-29225600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr22:29212000-29225200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr22:29213600-29220600	Enhancers	Primary T cells fromperipheralblood	blood
22	chr22:29214000-29218600	Enhancers	Liver	Liver
23	chr22:29214000-29219200	Enhancers	Pancreas	Pancrea
24	chr22:29214600-29217600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr22:29214600-29218400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr22:29214600-29222800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr22:29214600-29223000	Weak transcription	Fetal Stomach	stomach
28	chr22:29214800-29217600	Enhancers	Dnd41	blood
29	chr22:29214800-29217800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr22:29214800-29218600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr22:29214800-29218600	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr22:29214800-29242200	Weak transcription	Aorta	Aorta
33	chr22:29215000-29225200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr22:29215200-29217600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr22:29215200-29218800	Weak transcription	K562	blood
36	chr22:29215200-29219000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr22:29215200-29219000	Weak transcription	Brain Anterior Caudate	brain
38	chr22:29215200-29225200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr22:29215400-29225600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr22:29215600-29217000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr22:29215600-29217600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr22:29215600-29225600	Weak transcription	Fetal Muscle Leg	muscle
43	chr22:29215600-29231600	Weak transcription	Right Ventricle	heart
44	chr22:29215800-29217000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr22:29215800-29217000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr22:29215800-29217400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr22:29215800-29217600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr22:29215800-29218000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr22:29215800-29218800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr22:29215800-29225200	Weak transcription	Colon Smooth Muscle	Colon

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