Variant report

Variant	rs5754141
Chromosome Location	chr22:32936298-32936299
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:32933708..32937841-chr22:33196276..33199119,4	MCF-7	breast:
2	chr22:32928103..32930722-chr22:32934980..32936586,2	MCF-7	breast:
3	chr22:32935341..32940851-chr22:32952313..32956913,8	MCF-7	breast:
4	chr22:32934249..32936537-chr22:32956952..32958878,2	MCF-7	breast:
5	chr22:32936212..32939434-chr22:32941471..32944860,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100234	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs130448	0.80[CHD][hapmap]
rs130458	0.85[JPT][hapmap]
rs13055961	0.81[CHB][hapmap];0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2710373	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2710376	0.83[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4507	0.86[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]
rs4821072	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749459	0.85[ASN][1000 genomes]
rs5754135	0.85[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5754136	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5754143	0.83[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58033264	0.84[ASN][1000 genomes]
rs762907	0.83[CHB][hapmap];0.91[YRI][hapmap];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv914981	chr22:32912277-32940660	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5754141	PLA2G3	cis	parietal	SCAN
rs5754141	CABP7	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32928400-32937600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr22:32929000-32940800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr22:32931000-32937800	Weak transcription	Pancreas	Pancrea
4	chr22:32931000-32938200	Weak transcription	Colon Smooth Muscle	Colon
5	chr22:32931000-32938200	Weak transcription	Gastric	stomach
6	chr22:32931200-32937800	Weak transcription	Fetal Lung	lung
7	chr22:32932800-32937800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr22:32934200-32942200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr22:32934400-32936800	Enhancers	HepG2	liver
10	chr22:32934400-32937200	Enhancers	Placenta Amnion	Placenta Amnion
11	chr22:32934600-32936800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr22:32934800-32936600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr22:32934800-32937400	Enhancers	Hela-S3	cervix
14	chr22:32934800-32938400	Enhancers	Adipose Nuclei	Adipose
15	chr22:32934800-32939400	Enhancers	Fetal Muscle Leg	muscle
16	chr22:32935200-32936600	Enhancers	K562	blood
17	chr22:32935200-32942800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr22:32935400-32936400	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr22:32935400-32936600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr22:32935400-32936600	Enhancers	Placenta	Placenta
21	chr22:32935400-32936800	Enhancers	Fetal Muscle Trunk	muscle
22	chr22:32935400-32938200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr22:32935600-32936400	Enhancers	Fetal Intestine Large	intestine
24	chr22:32935600-32936400	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr22:32935600-32936600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr22:32935600-32936600	Enhancers	Fetal Thymus	thymus
27	chr22:32935600-32936800	Enhancers	Liver	Liver
28	chr22:32935600-32936800	Enhancers	Right Atrium	heart
29	chr22:32935600-32936800	Enhancers	HSMM	muscle
30	chr22:32935600-32936800	Enhancers	HSMMtube	muscle
31	chr22:32935600-32938400	Weak transcription	Fetal Heart	heart
32	chr22:32935800-32936400	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr22:32935800-32936400	Enhancers	GM12878-XiMat	blood
34	chr22:32935800-32936600	Enhancers	Lung	lung
35	chr22:32935800-32936600	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr22:32935800-32936600	Enhancers	Spleen	Spleen
37	chr22:32935800-32936800	Enhancers	Left Ventricle	heart
38	chr22:32935800-32938200	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr22:32935800-32938400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr22:32935800-32939600	Enhancers	Right Ventricle	heart
41	chr22:32936000-32936400	Enhancers	Duodenum Mucosa	Duodenum
42	chr22:32936200-32936600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr22:32936200-32936800	Enhancers	Colonic Mucosa	Colon
44	chr22:32936200-32938000	Weak transcription	Fetal Stomach	stomach
45	chr22:32936200-32941400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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