Variant report

Variant	rs132534
Chromosome Location	chr22:29299806-29299807
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29294042..29296336-chr22:29297392..29300176,2	MCF-7	breast:
2	chr22:29195884..29197508-chr22:29298766..29301210,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100219	Chromatin interaction
ENSG00000226471	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12165962	0.82[CEU][hapmap];0.82[TSI][hapmap]
rs132539	0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16986825	0.84[CHD][hapmap]
rs2239815	0.83[CEU][hapmap];0.85[TSI][hapmap]
rs2347447	0.85[TSI][hapmap]
rs3788409	0.85[TSI][hapmap]
rs469989	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]
rs5752797	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs5762795	0.83[CEU][hapmap];0.85[TSI][hapmap]
rs5762877	0.91[EUR][1000 genomes]
rs5997408	0.83[CEU][hapmap]
rs6005881	0.82[TSI][hapmap]
rs7287806	0.83[CEU][hapmap];0.85[TSI][hapmap]
rs7287918	0.83[ASW][hapmap]
rs739196	0.84[CHD][hapmap]
rs763073	0.83[CEU][hapmap];0.85[TSI][hapmap]
rs8141529	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[MKK][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs132534	GAL3ST1	cis	cerebellum	SCAN
rs132534	XBP1	Cis_1M	lymphoblastoid	RTeQTL
rs132534	XBP1	cis	cerebellum	SCAN
rs132534	MN1	cis	cerebellum	SCAN
rs132534	BEND4	trans	parietal	SCAN
rs132534	ZNRF3	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29288000-29301800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr22:29291200-29300600	Weak transcription	Psoas Muscle	Psoas
3	chr22:29292400-29300600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr22:29295600-29300600	Weak transcription	Brain Substantia Nigra	brain
5	chr22:29295800-29300200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr22:29296200-29300400	Weak transcription	HSMMtube	muscle
7	chr22:29296400-29300400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr22:29296600-29300000	Weak transcription	Osteobl	bone
9	chr22:29296600-29300400	Weak transcription	HSMM	muscle
10	chr22:29296800-29310200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr22:29297400-29300600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr22:29298200-29301000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr22:29298400-29301200	Enhancers	Adipose Nuclei	Adipose
14	chr22:29298400-29301200	Enhancers	Fetal Muscle Leg	muscle
15	chr22:29298400-29301400	Enhancers	Right Ventricle	heart
16	chr22:29298400-29302800	Enhancers	Liver	Liver
17	chr22:29298400-29308400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr22:29298400-29310400	Enhancers	Fetal Intestine Large	intestine
19	chr22:29298600-29300000	Enhancers	H9 Cell Line	embryonic stem cell
20	chr22:29298600-29300200	Genic enhancers	HepG2	liver
21	chr22:29298600-29300200	Enhancers	HMEC	breast
22	chr22:29298600-29300800	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr22:29298600-29300800	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr22:29298600-29300800	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr22:29298600-29301000	Enhancers	Duodenum Mucosa	Duodenum
26	chr22:29298600-29301200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr22:29298600-29302000	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr22:29298600-29302400	Enhancers	Placenta	Placenta
29	chr22:29298600-29302600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr22:29298600-29302600	Enhancers	Fetal Lung	lung
31	chr22:29298600-29302800	Enhancers	Fetal Kidney	kidney
32	chr22:29298600-29304600	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr22:29298600-29305000	Enhancers	Brain Anterior Caudate	brain
34	chr22:29298600-29305400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr22:29298800-29300000	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr22:29298800-29300000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr22:29298800-29300000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr22:29298800-29301000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr22:29298800-29301200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr22:29298800-29301200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr22:29298800-29301200	Enhancers	Fetal Heart	heart
42	chr22:29298800-29302000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr22:29298800-29302800	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr22:29298800-29302800	Enhancers	Rectal Smooth Muscle	rectum
45	chr22:29298800-29304400	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr22:29298800-29305200	Enhancers	Brain Cingulate Gyrus	brain
47	chr22:29299000-29300000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr22:29299000-29300000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr22:29299000-29300000	Enhancers	Fetal Muscle Trunk	muscle
50	chr22:29299000-29300000	Enhancers	Gastric	stomach

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